Re: [gmx-users] Re: g_analyze
Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.com wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
Hi, I tried g_select to dump the structure with the interacting water molecules, but I don't know know how to do that. I searched for some threads in the discussion but wasn't able to find anything related to my need. Can you explain how can I do that ? On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta bharat.85.m...@gmail.comwrote: Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.com wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx
Re: [gmx-users] Re: g_analyze
Thanks justin for your replies. I understood the g_analyze related data. I tired g_analyze to dump the structures as you said. But, I didn't find any switch that can be used to dump the structure in pdb format. On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/13 6:56 PM, bharat gupta wrote: Hi, I tried g_select to dump the structure with the interacting water molecules, but I don't know know how to do that. I searched for some threads in the discussion but wasn't able to find anything related to my need. Can you explain how can I do that ? Start with g_select -select 'help all' and see what you can determine. Such selections are rather straightforward and have been explained several times on the list. If you need help, show us what you're doing and describe why it isn't what you want. It will ultimately save a lot of time. -Justin On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta bharat.85.m...@gmail.com wrote: Sorry, I attached the wrong file . Here's the average file generate from one of the files I sent in my last mail. I used the command g_analyze -f hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained from this command :- https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg Now, if you see, the graph (in previous mail) and average file, both correlates well. I have a doubt about interpreting the result from g_analyze. The value 7.150740e+00 implies that on average 7 hydrogen bonds are formed during the simulation time of 5ns to 10ns. What does then the average file or its graph tells ?? On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/11/13 4:06 AM, bharat gupta wrote: In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg Neither of these files produce output that corresponds to the PNG image above. Both files have values in 6-9 H-bond range and thus agree with the g_analyze output, which I can reproduce. I suspect you're somehow getting your files mixed up. -Justin On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.com wrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before
Re: [gmx-users] Re: g_analyze
In addition to my previous question, I have another question about g_analyze. When I used the hbond.xvg file to get the average and plotted the average.xvg file I found that the average value is round 4 to 5 according to the graph. But g_analyze in its final calculation gives 7.150 as the average values... Here's the link for the graph and result of average value calculated by g_analyze :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.0620.163 SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.4950.153 https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png Here's the link hbond.xvg file and its averaged file https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta bharat.85.m...@gmail.comwrote: thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? Thanks --- BHARAT On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 12:20 AM, bharat gupta wrote: Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. Hard to say, but I've never known g_analyze to be wrong, so I'd suspect something is amiss in your manual calculation. The difference between 13.5 and 0.0069 is huge; you should be able to scan through the data file to see what the expected value should be. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Data sets 1 and 2. You will note that there are two columns of data in the -hbnum output produced by g_hbond, with titles explaining both. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 7:18 PM, bharat gupta wrote: I checked the file hbnum.xvg file and it contains three columns - time, hbonds, hbonds that donot follow the angle criteria. In that case SS1 is The third column is not actually H-bonds, then ;) the average of actual hbonds (2nd column ) and SS2 is the average of 3rd column. Am I right here or not ?? Yes. I tried to calculate the h-bond for residues 115-118 individually, and then checked the average for each residue. For single residue calculation, the g_analyze average value is correct. But when I calculate the h-bond as a range 115-118, I get the g_analyze value as 1.62 . I calculated the average manually in excel, got the average values as 16.2 [which is (g_analyze avg value)/10]. That is impossible. You cannot get a different average by examining the same numbers. Read the g_analyze output again - I am willing to bet that you're not seeing the exponent of the scientific notation. I then added up the average values of h-bonds of individual residues and the final comes around 16.2, same as that of the 115-118 range h-bonds. This means that my calculation is correct. I also used trjorder to calculate h-bond at distance 0.34 for residues 115-118. I got the average value around 2.51 from g_analyze, where as manual calculation gives 25.1. I don't knw why for the range the g_analyze give avg as (actual avg value)/10 ?? Why does trjorder and g_hbond gives different number of hydrogen bonds for the same residue set?? All of this comes down to correctly reading the screen output. I have no idea what you're doing with trjorder, though. It doesn't measure H-bonds. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_analyze
thank you informing about g_rdf... Is it possible to dump the structure with those average water molecules interacting with the residues. I generated the hbond.log file which gives the details but I need to generate a figure for this ?? On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:38 PM, bharat gupta wrote: But trjorder can be used to calculate the hydration layer or shell around residues ... Right ?? Yes, but I also tend to think that integrating an RDF is also a more straightforward way of doing that. With trjorder, you set some arbitrary cutoff that may or may not be an informed decision - with an RDF it is clear where the hydration layers are. -Justin On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/10/13 8:30 PM, bharat gupta wrote: Thanks for your reply. I was missing the scientific notation part. Now everything is fine. Regarding trjorder, it doesn't measure h-bonds but gives the water nearest to protein. I wouldn't try to draw any sort of comparison between the output of trjorder and g_hbond. If you want to measure H-bonds, there's only one tool for that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_analyze
Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Please clarify these doubts.. Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Using mpirun on CentOS 6.0
Hi, I am getting the following error while using the command - [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt Error - /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255 I complied gromacs using - ./configure --enable-shared --enable-mpi. I have installed the mpich package , this is what I get when I check for mpirun and mpiexec - [root@localhost /]# which mpirun /usr/bin/mpirun [root@localhost /]# which mpiexec /usr/bin/mpiexec What could be the problem here ?? Thanks Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Calculation of water density around certain protein residues
Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg In the output, I got for each time step I some number of residues. For eg, @ s0 legend Nearby water 0.000 159.000 0.200 168.000 0.400 173.000 0.600 171.000 Can I get the average the number of water moleculed for the entire simulation time ?? and how can I get the density instead of number ?? Pls respond to this query ... Thanks -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... Thanks in advance for help Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculation of water density around certain protein residues
Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg In the output, I got for each time step I some number of residues. For eg, @ s0 legend Nearby water 0.000 159.000 0.200 168.000 0.400 173.000 0.600 171.000 Can I get the average the number of water moleculed for the entire simulation time ?? and how can I get the density instead of number ?? Pls respond to this query ... Thanks -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... Thanks in advance for help Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Using gromacs on Rocks cluster
Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Using gromacs on Rocks cluster
Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] script to add water in protein
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On Mon, Aug 12, 2013 at 4:09 PM, pooja_gu...@nccs.res.in wrote: Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for the advice. I have not understood the things properly, especially the convergence of REMD. I got two relevant papers : 1. Convergence of replica exchange molecular dynamics 2. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. If you can provide better reference then this ... Thank you francesco for the option. Indeed I was missing a a very imp. option while plotting the data. On Fri, May 24, 2013 at 7:40 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi to everybody, Bharat, maybe i didn't follow exactly the wole tale, but is it possible you are running xmgrace without the -nxy option? You are probably visualizing the data related the 1st replica several times! Francesco 2013/5/24 Mark Abraham mark.j.abra...@gmail.com On Fri, May 24, 2013 at 10:44 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. No, if the rows of both matrices describe time, and there are two different matrices for the same exchange set, then the information described by a column must differ, like I said last email. You are applying the same interpretation to a column from either matrix. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? I've answered this question several times. Each replica merely visiting each temperature means nothing for converged sampling. There's lots of literature here, including stuff by me ;-) A balance of replicas visiting ensembles is necessary but not sufficient for the kind of replica flow that would be necessary for generalized convergence. One can shrug one's shoulders at some point and say things are probably as good as they'll get for reasonable cost, but your reviewer might disagree with you. Convergence of sampling at a single temperature can be assessed in a similar way as for non-REMD simulations, caveat that the exchange events pretty much stop you using metrics based on correlation time. If you want to know how to do things properly, you need to do some reading. Mark On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
I checked the first 5 md.log files, and the data is exactly the same in all of them Does it mean there could be problem with demux.pl On Thu, May 23, 2013 at 3:53 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written that way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png On Thu, May 23, 2013 at 5:21 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Each md.log has all the information about all replica exchanges, as you can see. I suggested you look at your .log and .xvg files a week ago ;-) There's no problem if a script post-processes all the identical information from each .log file. Mark On Thu, May 23, 2013 at 9:01 AM, bharat gupta bharat.85.m...@gmail.com wrote: I checked the first 5 md.log files, and the data is exactly the same in all of them Does it mean there could be problem with demux.pl On Thu, May 23, 2013 at 3:53 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http
Re: [gmx-users] Re: REMD analysis
Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.comwrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD analysis
Dear Sir, I performed another round of trial with different set of temperature and I got the avg accp. ration around 0.22. Here's the temp. dist. that I used : 250 268 288 308 331 355 380 408 438 469 503 540 579 621 I then checked the replica_index and replica_temp files for each replica individually. The plots are exactly similar for all the replicas, as an eg. here's the link for first three replicas . https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.pnghttps://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png;cid=1368714426780-10 https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.pnghttps://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png;cid=1368714426780-10 https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.pnghttps://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png;cid=1368714426780-10 https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.pnghttps://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png;cid=1368714426780-10 https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.pnghttps://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png;cid=1368714426780-10 https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.pnghttps://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png;cid=1368714426780-10 I checked the PE overlap also, that looks fine ( https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.pnghttps://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png;cid=1368714426780-10 ) I checked for the temp. dist. which also looks fine to me . https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.pnghttps://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png;cid=1368714426780-10 I don't know why all plots are similar ?? Is this related to wrong settings in mdp file. Here's the mdp file that I am using for production run. I changed ref_t for each replica in the mdp file. define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps nsteps = 2500; 5 ps = 50 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 250 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 78.5; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = 0.005 I suspect that I am doing something wrong somewhere ... It will be helpful if anybody can help me in this regard... Regards -- BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD analysis
Dear Sir, I performed another round of trial with different set of temperature and I got the avg accp. ration around 0.22. Here's the temp. dist. that I used : 250 268 288 308 331 355 380 408 438 469 503 540 579 621 I then checked the replica_index and replica_temp files for each replica individually. The plots are exactly similar for all the replicas, as an eg. here's the link for first three replicas . https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png I checked the PE overlap also, that looks fine ( https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png) I checked for the temp. dist. which also looks fine to me . https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png I don't know why all plots are similar ?? Is this related to wrong settings in mdp file. Here's the mdp file that I am using for production run. I changed ref_t for each replica in the mdp file. I suspect that I am doing something wrong somewhere ... define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps nsteps = 2500; 5 ps = 50 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 250 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 78.5; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = 0.005 It will be helpful if you provide your comments... Regards -- BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, My main objective of carrying out REMD is to study peptide folding and if possible to get some insight in protein design and folding. I read some articles related to my work and they always show temp (replica_index) graphs for 2-3 replicas , saying that the sufficient sampling had been achieved. In my case I checked the replica_temp for first three replicas ( https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) Almost all the three graphs are similar and the last 15ns shows that there is no enough exchange (if I have analyzed correctly) ?? In this case the acceptance ratio was fine and PE overlap was also good, but problem lies with efficient sampling ?? What shall I do in such a case ?? On Sat, May 18, 2013 at 12:27 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, May 17, 2013 at 4:26 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. That's nice. You need to decide what you need to do about it if you want graphs that look like those you see reported :-) Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? Ah, now here's the real question :-) Spacing the replicas for optimal *flow* is a difficult problem, even for toy peptides, see e.g. papers by Nadler and Hansmann. Merely accepting exchanges does not imply flow. The belief is that getting flow enhances sampling, but the latter is hard to demonstrate without showing that simulation time to converged sampling actually reduces. I'm not aware of anybody who's actually done that - but it would certainly be an advantage if your application is interested in data at a range of temperatures. Mark On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg ). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
[gmx-users] Re: REMD analysis
Dear Sir, I ran the REMD simulation with temp. distribution discussed in my last thread. Each replica was run for 50 ns Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 Repl .22 .19 .18 .16 .19 .21 .23 .25 .26 .29 .28 .28 Repl number of exchanges: Repl 0123456789 10 11 12 Repl 2661 2369 2296 2008 2360 2668 2866 3119 3234 3549 3469 3475 Repl average number of exchanges: Repl 0123456789 10 11 12 Repl .21 .19 .18 .16 .19 .21 .23 .25 .26 .28 .28 .28 Now, how to find the potential energy overlap for each replica??.. I have obtained the pot. energy for each replica separately.. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD analysis
Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution (https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [Spam:*****] [gmx-users] REMD analysis
Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges
Re: [Spam:*****] [gmx-users] REMD analysis
Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want
Re: [gmx-users] REMD analysis
Okay, now I can start with large production runs . On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s
Re: [Spam:*****] [gmx-users] REMD analysis
Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456978 10 11 12 6 1023459678 10 11 12 8 1203495768 10 11 12 10 1230947568 11 10 12 replica_temp 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456897 10 11 12 6 1023457896 10 11 12 8 2013468795 10 11 12 10 3012578694 11 10 12 On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing
Re: [Spam:*****] [gmx-users] REMD analysis
The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks
[gmx-users] REMD analysis
Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [Spam:*****] [gmx-users] REMD analysis
Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD average acceptance ratio
Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD average acceptance ratio
Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list
Re: [gmx-users] REMD average acceptance ratio
Dear Sir, I tried again with the following temp. ditribution, this time with 30 replicas (280 K -624K) and 500 ps simulation time for each one. 0 280 1 287.8 2 295.9 3 304.2 4 312.7 5 321.5 6 330.5 7 339.8 8 349.3 9 359.1 10 369.1 11 379.5 12 390.1 13 401.0 14 412.3 15 423.8 16 435.7 17 447.9 18 460.4 19 473.3 20 486.6 21 500.2 22 514.3 23 528.7 24 543.5 25 558.7 26 574.4 27 590.4 28 607.0 29 624.0 The output of md29.log file is :- Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .68 .63 .62 .68 .71 .66 .69 .68 .71 .67 .64 .71 .69 .71 .66 .69 .73 .73 .72 .73 .69 .71 .71 .74 .73 .70 .72 .74 .71 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl 81 77 79 90 93 78 91 80 88 78 81 92 96 94 81 83 90 92 83 97 89 87 91 94 88 84 85 89 86 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .65 .62 .63 .73 .74 .63 .73 .65 .70 .63 .65 .74 .77 .76 .65 .67 .72 .74 .66 .78 .71 .70 .73 .76 .70 .68 .68 .72 .69 The average acceptance ration comes around 0.69 , which is very high. Now, in order to get the avg. acceptance ration between 0.2 to 0.3 and also all the replicas should exchange , what has to be done. Here's the link for remd_index and remd_temp files https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png I want to that if I include water for the simulation, the same temp. distribution would work or not ?? On Sun, May 12, 2013 at 12:10 AM, XAvier Periole x.peri...@rug.nl wrote: You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789
[gmx-users] Re: REMD average acceptance ratio
Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.pnghttps://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mhttps://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD analysis
Dear gmx members, I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs mpi error while running REMD
Dear gmx-users, I got the following error after issuing the final command for running 12 replicas :- [bme:42039] *** Process received signal *** [bme:42039] Signal: Segmentation fault (11) [bme:42039] Signal code: Invalid permissions (2) [bme:42039] Failing at address: 0x7f093b655340 [bme:42039] [ 0] /lib64/libpthread.so.0() [0x329220f500] [bme:42039] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x2337) [0x7f093c281fa7] [bme:42039] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f093c2175d6] [bme:42039] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f093ca47b3a] [bme:42039] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f093cadc6f7] [bme:42039] [ 5] mdrun(do_md+0x6a45) [0x42c245] [bme:42039] [ 6] mdrun(mdrunner+0xa59) [0x421309] [bme:42039] [ 7] mdrun(main+0x12fd) [0x4317dd] [bme:42039] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd] [bme:42039] [ 9] mdrun() [0x405a29] [bme:42039] *** End of error message *** Wrote pdb files with previous and current coordinates [bme:42036] *** Process received signal *** [bme:42036] Signal: Segmentation fault (11) [bme:42036] Signal code: Invalid permissions (2) [bme:42036] Failing at address: 0x7f794bbe3800 [bme:42036] [ 0] /lib64/libpthread.so.0() [0x329220f500] [bme:42036] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x13e2) [0x7f794c4b8052] [bme:42036] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f794c44e5d6] [bme:42036] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f794cc7eb3a] [bme:42036] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f794cd136f7] [bme:42036] [ 5] mdrun(do_md+0x6a45) [0x42c245] [bme:42036] [ 6] mdrun(mdrunner+0xa59) [0x421309] [bme:42036] [ 7] mdrun(main+0x12fd) [0x4317dd] [bme:42036] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd] [bme:42036] [ 9] mdrun() [0x405a29] [bme:42036] *** End of error message *** [bme:42042] *** Process received signal *** [bme:42042] Signal: Segmentation fault (11) [bme:42042] Signal code: Address not mapped (1) [bme:42042] Failing at address: 0x7f119c3b96b0 [bme:42042] [ 0] /lib64/libpthread.so.0() [0x329220f500] [bme:42042] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1345) [0x7f11972e2fb5] [bme:42042] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96) [0x7f11972795d6] [bme:42042] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa) [0x7f1197aa9b3a] [bme:42042] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7) [0x7f1197b3e6f7] [bme:42042] [ 5] mdrun(do_md+0x6a45) [0x42c245] [bme:42042] [ 6] mdrun(mdrunner+0xa59) [0x421309] [bme:42042] [ 7] mdrun(main+0x12fd) [0x4317dd] [bme:42042] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd] [bme:42042] [ 9] mdrun() [0x405a29] [bme:42042] *** End of error message *** -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: Selecting the temperature distribution
I think it should be me who should be sorry. I should have asked the question again in the forum without referring to some particular individual. On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.comwrote: 2013/4/24 Justin Lemkul jalem...@vt.edu I haven't said anything because I agree with what Massimo has already told you. If that is comforting in some way to know, then so be it, but I think it is rather rude to suggest that you would rather someone else answer your question, even after being given thorough and correct insight. This is a community forum with many experts who have valuable insight to share. Well, he couldn't know that my insight was right (honestly, I was expecting to be corrected!). I think he did right by trying to be double-sure, I don't feel offended by it :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Selecting the temperature distribution
Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? - Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Selecting the temperature distribution
Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: Selecting the temperature distribution
I have got the temperature distribution from the same link, but how to select evenly spaced temperatures for 56 replicas, I need to know that On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.comwrote: Look here: http://folding.bmc.uu.se/remd/ 2013/4/23 bharat gupta bharat.85.m...@gmail.com Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: Selecting the temperature distribution
Sorry for that, I explain it again. Actually, I used the this link to generate a temp. distribution. But I can do REMD for 56 replicas only, as I have 56 processors available. The t-remd calculator provides 220 temperature values : 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17, 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56, 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18, 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04, 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13, 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47, 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05, 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90, 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00, 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38, 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05, 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03, 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26, 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79, 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63, 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80, 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27, 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07, 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24, 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73, 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56, 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76, 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47, 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44, 595.24, 597.04, 598.85, 600.66 Now, how can I temp. from these, so that the replicas can exchange ... On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.comwrote: I don't understand your question. If you got the temperature distribution, what else do you need? 2013/4/23 bharat gupta bharat.85.m...@gmail.com I have got the temperature distribution from the same link, but how to select evenly spaced temperatures for 56 replicas, I need to know that On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.com wrote: Look here: http://folding.bmc.uu.se/remd/ 2013/4/23 bharat gupta bharat.85.m...@gmail.com Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http
Re: [gmx-users] Fwd: Selecting the temperature distribution
But if I choose a smaller temperature range , would it be possible to observe any folding event ?? On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.comwrote: Thanks, now it's clearer. Now, how can I temp. from these, so that the replicas can exchange ... You can't, I would say. The system you have requires so many replicas to exchange properly from the two temperature extremes you set up. As you have seen, if you pick up temperatures in that range randomly, they can't exchange anymore. They are too far away. I would choose a smaller temperature range. There is little else you can do, I think. 2013/4/23 bharat gupta bharat.85.m...@gmail.com Sorry for that, I explain it again. Actually, I used the this link to generate a temp. distribution. But I can do REMD for 56 replicas only, as I have 56 processors available. The t-remd calculator provides 220 temperature values : 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17, 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56, 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18, 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04, 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13, 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47, 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05, 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90, 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00, 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38, 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05, 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03, 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26, 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79, 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63, 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80, 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27, 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07, 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24, 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73, 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56, 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76, 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47, 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44, 595.24, 597.04, 598.85, 600.66 Now, how can I temp. from these, so that the replicas can exchange ... On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.com wrote: I don't understand your question. If you got the temperature distribution, what else do you need? 2013/4/23 bharat gupta bharat.85.m...@gmail.com I have got the temperature distribution from the same link, but how to select evenly spaced temperatures for 56 replicas, I need to know that On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.com wrote: Look here: http://folding.bmc.uu.se/remd/ 2013/4/23 bharat gupta bharat.85.m...@gmail.com Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support
Re: [gmx-users] Fwd: Selecting the temperature distribution
So, my final question is whether is possible to do REMD for my system, using the computational resource that I have. On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.comwrote: Who knows? It depends on the size of your peptide, on the energy landscape, on how long is the run you plan to do. I would bet on no, however. 2013/4/23 bharat gupta bharat.85.m...@gmail.com But if I choose a smaller temperature range , would it be possible to observe any folding event ?? On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com wrote: Thanks, now it's clearer. Now, how can I temp. from these, so that the replicas can exchange ... You can't, I would say. The system you have requires so many replicas to exchange properly from the two temperature extremes you set up. As you have seen, if you pick up temperatures in that range randomly, they can't exchange anymore. They are too far away. I would choose a smaller temperature range. There is little else you can do, I think. 2013/4/23 bharat gupta bharat.85.m...@gmail.com Sorry for that, I explain it again. Actually, I used the this link to generate a temp. distribution. But I can do REMD for 56 replicas only, as I have 56 processors available. The t-remd calculator provides 220 temperature values : 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17, 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56, 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18, 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04, 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13, 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47, 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05, 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90, 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00, 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38, 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05, 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03, 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26, 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79, 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63, 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80, 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27, 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07, 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24, 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73, 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56, 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76, 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47, 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44, 595.24, 597.04, 598.85, 600.66 Now, how can I temp. from these, so that the replicas can exchange ... On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal deviceran...@gmail.com wrote: I don't understand your question. If you got the temperature distribution, what else do you need? 2013/4/23 bharat gupta bharat.85.m...@gmail.com I have got the temperature distribution from the same link, but how to select evenly spaced temperatures for 56 replicas, I need to know that On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal deviceran...@gmail.com wrote: Look here: http://folding.bmc.uu.se/remd/ 2013/4/23 bharat gupta bharat.85.m...@gmail.com Dear gmx users, I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas. I randomly chose some temp distribution and the exchange probabilities was 0.0. I know that we can use the formula Ti=T0*ek*i, but what is the value for i and K here ?? BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support
Re: [gmx-users] Fwd: Selecting the temperature distribution
Thanks a lot for your prompt responses. By using implicit solvent , I am getting on 9 temperature values. I think this should work , I will try it out. Also, i checked that when the no. of water molecules are reduced , the no. of temp. values are also reduced. If I reduce the no. of water molecules or reduce the size of box , will it help. As of now I am using octahedron box. On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.comwrote: It depends on what you want to do. Possible it is certainly possible, but you can't be guaranteed to observe the conformational changes you desire to observe. Again, it does not depend only on the REMD, but also on the length of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends on your system itself -and this you cannot know without trying. If you want to improve sampling beyond what standard REMD can do, to exploit your computational resources at the best, you can look into other approaches like solute tempering ( http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics ( http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study *well* this kind of things, talk with experts in these techniques, and remember that there is no guarantee any of them will bring the result you want. Good luck! :) 2013/4/23 bharat gupta bharat.85.m...@gmail.com So, my final question is whether is possible to do REMD for my system, using the computational resource that I have. On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.com wrote: Who knows? It depends on the size of your peptide, on the energy landscape, on how long is the run you plan to do. I would bet on no, however. 2013/4/23 bharat gupta bharat.85.m...@gmail.com But if I choose a smaller temperature range , would it be possible to observe any folding event ?? On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com wrote: Thanks, now it's clearer. Now, how can I temp. from these, so that the replicas can exchange ... You can't, I would say. The system you have requires so many replicas to exchange properly from the two temperature extremes you set up. As you have seen, if you pick up temperatures in that range randomly, they can't exchange anymore. They are too far away. I would choose a smaller temperature range. There is little else you can do, I think. 2013/4/23 bharat gupta bharat.85.m...@gmail.com Sorry for that, I explain it again. Actually, I used the this link to generate a temp. distribution. But I can do REMD for 56 replicas only, as I have 56 processors available. The t-remd calculator provides 220 temperature values : 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 308.17, 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50, 317.56, 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10, 327.18, 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93, 337.04, 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00, 347.13, 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31, 357.47, 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86, 368.05, 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68, 378.90, 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75, 390.00, 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10, 401.38, 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74, 413.05, 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68, 425.03, 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89, 437.26, 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38, 449.79, 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18, 462.63, 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32, 475.80, 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76, 489.27, 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52, 503.07, 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65, 517.24, 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10, 531.73, 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90, 546.56, 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06, 561.76, 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60, 577.47, 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65, 593.44, 595.24, 597.04, 598.85, 600.66 Now, how can I temp. from these, so that the replicas can exchange ... On Tue, Apr 23, 2013 at 9:04 PM
Re: [gmx-users] Fwd: Selecting the temperature distribution
Dear Justin/Mark, I have asked this question previously in the forum, I got some reply from other members. It will be more useful if you can provide you expert comments on the same. I am planning to run REMD for a peptide (406 atoms )+ solvent system (27639). The temperature range I selected is from 300 to 500. I want to select appropriate temp. for 56 replicas (as I have 56 processors available). I used the t-remd calculator for temp. generation. It provided some 200 temp. values. Here are my questions : 1. Is it possible to select equally spaced temp. values from those values ?? 2. I checked that reducing the no. of water mol. decreases the temp. values. What if I reduce the no. of water mol., will if affect the simulation ?? On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal deviceran...@gmail.comwrote: In general, the smaller is your system, the less temperatures you will need (and you'll have better performance). Notice however that implicit solvent, while surely a possibility worth considering, is not usually considered to be very good -take care that if you write a paper from implicit solvent results, reviewers might not be happy. There is a chance that the results coming out of your simulation might be nonsense. Discuss this choice with your supervisor and/or with expert colleagues who know about limitations of implicit solvent. You need to be able to justify your choice scientifically -for example testing it with a known,similar system and observing that implicit solvent reproduces the behaviour of that system in explicit solvent well. About reducing the box size, by all means try it, but always make sure it is large enough to avoid that the periodic copies of your molecule see each other. See http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand be sure to understand it. 2013/4/23 bharat gupta bharat.85.m...@gmail.com Thanks a lot for your prompt responses. By using implicit solvent , I am getting on 9 temperature values. I think this should work , I will try it out. Also, i checked that when the no. of water molecules are reduced , the no. of temp. values are also reduced. If I reduce the no. of water molecules or reduce the size of box , will it help. As of now I am using octahedron box. On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal deviceran...@gmail.com wrote: It depends on what you want to do. Possible it is certainly possible, but you can't be guaranteed to observe the conformational changes you desire to observe. Again, it does not depend only on the REMD, but also on the length of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depends on your system itself -and this you cannot know without trying. If you want to improve sampling beyond what standard REMD can do, to exploit your computational resources at the best, you can look into other approaches like solute tempering ( http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics ( http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to study *well* this kind of things, talk with experts in these techniques, and remember that there is no guarantee any of them will bring the result you want. Good luck! :) 2013/4/23 bharat gupta bharat.85.m...@gmail.com So, my final question is whether is possible to do REMD for my system, using the computational resource that I have. On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal deviceran...@gmail.com wrote: Who knows? It depends on the size of your peptide, on the energy landscape, on how long is the run you plan to do. I would bet on no, however. 2013/4/23 bharat gupta bharat.85.m...@gmail.com But if I choose a smaller temperature range , would it be possible to observe any folding event ?? On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal deviceran...@gmail.com wrote: Thanks, now it's clearer. Now, how can I temp. from these, so that the replicas can exchange ... You can't, I would say. The system you have requires so many replicas to exchange properly from the two temperature extremes you set up. As you have seen, if you pick up temperatures in that range randomly, they can't exchange anymore. They are too far away. I would choose a smaller temperature range. There is little else you can do, I think. 2013/4/23 bharat gupta bharat.85.m...@gmail.com Sorry for that, I explain it again. Actually, I used the this link to generate a temp. distribution. But I can do REMD for 56 replicas only, as I have 56 processors available. The t-remd calculator provides 220 temperature values
Re: [gmx-users] Green fluorescent protein's chromophore
Hi, You can refer this paper for the topology http://pubs.acs.org/doi/abs/10.1021/jp014476w. --- BHARAT On Wed, Dec 5, 2012 at 10:14 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'm looking for the model as well as for the pre-paired topology for any kind of GFP protein with the chromophore group covaletnly bonded in the interiour of that protein. Some times ago I've tried to make such models by hands but I've forced with some difficulties with the integration of the chromophore group to the existing GROMOS force field parameter files. In that case I had .itp for the chromophore group made by PRODRG which I've failed to convert to the rtp and integrate to other files in accordance to the http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field So I'll be very thankfull if any could provide me with such model as well as suitable topology which I could use as the example for preparation of my future models :) Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculate Density with respect to time...
Hi, There's a plugin in VMD called volmap which I think can be used for this kind of analysis. Bharat On Sat, Sep 29, 2012 at 9:27 PM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs Users, I did simulation of two random coil peptides for 100ns. after 70 ns these peptide get converted to anti parallel beta sheet structure. I am interested to see the water density in between these peptides w.r.t. to time change And at the same time the distance between the peptide.. I found out the distance between peptide by g_mindist but I not found the appropriate way to calculate density of water with respect to time between two peptides.. I used g_density but it not gave me the information as per my need. Is there any way to solve these problem. Thank you in advance.. With best wishes and regards.. Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Peptide folding simulation
Hi, I have been trying to study folding of a peptide 24 residues long. I did a simulation of 50 ns with explicit solvent, CHARMM FF, but I was not able to find even a single folding event. Then I decided use explicit solvent for simulation and I again simulated the peptide for 100 ns . This time again I ended with no folding events. I know that in case of explicit solvent , a 50ns simulation time is not enough to observe anything. But I did it to see the initial behavior of the peptide in water. In take many random like conformation but doesnot fold into a desired beta-hairpin. For the explicit solvent simulation, I followed the lysozyme tutorial parameters. For implicit solvent simulation, I used the following parameters for Energy minimization : define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = Protein optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 For MD I used the following : - define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 10 ; 10 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 So, finally I want to know where have I gone in my simulation experiments, both implicit and explicit ?? ... Please reply . BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dihedral restraints
Hi, I tried restraining two residues of my peptide . The restraints were added after dihedrals in the top file. Here's how the .top file looks : [ dihedrals ] ; aiajakal functc0c1 c2c3 16 41817 2 18162019 2 25222726 2 25272226 2 27252928 2 27252829 2 30203231 2 32303433 2 37343938 2 39374140 2 48465049 2 48504649 2 50485251 2 50524851 2 52475053 2 52504753 2 54415655 2 [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 16 18 2030 1 1 -60 0 5 2 ; psi N - CA - C' - N(n+1) 18 2030 32 1 1 -30 0 5 2 ; phi C'(n-1) - N - CA - C' 30 32 3437 1 1 -90 0 5 2 ; psi N - CA - C' - N(n+1) 323437 39 17 1 1 0 0 5 2 I am getting the following error when I used the grompp command :- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 4, expected 5 or 5 for Dih. Rest.. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Fill Your Space So Sweet (F. Apple) Where did I do the mistake , can anybody guide me in this regard ?? , Also I don't know what should be the value for power and kfac , what I need is that the angles should be restrained to what I mentioned in file. Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dihedral restraints
Hi, I tried restraining two residues of my peptide . The restraints were added after dihedrals in the top file. Here's how the .top file looks : [ dihedrals ] ; aiajakal functc0c1 c2c3 16 41817 2 18162019 2 25222726 2 25272226 2 27252928 2 27252829 2 30203231 2 32303433 2 37343938 2 39374140 2 48465049 2 48504649 2 50485251 2 50524851 2 52475053 2 52504753 2 54415655 2 [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 16 18 2030 1 1 -60 0 5 2 ; psi N - CA - C' - N(n+1) 18 2030 32 1 1 -30 0 5 2 ; phi C'(n-1) - N - CA - C' 30 32 3437 1 1 -90 0 5 2 ; psi N - CA - C' - N(n+1) 323437 39 17 1 1 0 0 5 2 I am getting the following error when I used the grompp command :- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 4, expected 5 or 5 for Dih. Rest.. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You Fill Your Space So Sweet (F. Apple) Where did I do the mistake , can anybody guide me in this regard ?? , Also I don't know what should be the value for power and kfac , what I need is that the angles should be restrained to what I mentioned in file. Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Dihedral Constraints
Hi, This query is related to my previous queries. I want to constraint the psi/psi angle of the turn residue of my beta-hairpin , meaning that they are allowed to move in certain range of psi/phi angle space. Simultaneously, I want to freeze the movement of strand residues. This procedure has to be followed during minimization alone. From the previous answers to my queries I understood how to constrain dihedral space, but I don't know how to fix the movement of strand residues ?? ... any help will be highly appreciated. On Thu, Jun 14, 2012 at 4:24 PM, bharat gupta bharat.85.m...@gmail.comwrote: Sorry for the last reply, I wrote turns with different sequences wrongly, it's actually the turn with different dihedral constraints. I searched the gromacs user list , where I found this link , regarding calculation of dihedral energy of selected residues. I want to know whether this method would be useful ?? On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 4:57 PM, bharat gupta wrote: I am not going to compare this with anything , I have to look for sequences and their corresponding energies and select the lowest scoring ones. You can't compare total energies of different sequences and get a meaningful answer. What's the difference in energy between an apple and an orange mean? You can compare the average energy of an apple cut into pieces with the average energy of a whole apple, but that doesn't necessarily relate to the same quantity measured for an orange, either. There's a lot of work in measuring a decent *free* energy difference between some states. I request you to kindly elaborate on freezing some portion of the protein. ( I am bit confused as in my case I am fixing the dihedral of turn residues which means constraining them simultaneously I want to freeze the other region of the protein. ) You need to read the link I gave last time and use constraints and restraints in the accepted GROMACS sense in order for people to be able to understand your meaning clearly. There are links there to the kind of methods that are available. I think you need to do some reading and thinking about those :-) If you lock down all the degrees of freedom then you can't measure anything relevant. Mark On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 4:38 PM, bharat gupta wrote: Thanks Sir for the reply... This question is related to my first query that if we constraint the dihedral of the turn residue how can we fix/freeze the movement of other residues. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints As I am interested in only getting the energy of the hairpin when the turn residues are constrained within a particular phi psi angle range .. and with what are you going to compare those energies? And what will that comparison mean? Mark On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 12:04 PM, bharat gupta wrote: Thanks for the reply . Is it possible to calculate the dihedral energy of certain residues, like in my case for turn residues ??.. How can that be done First, seek to define dihedral energy... Force fields are not parametrized such that parts of them are expected to correlate with observables. This another question is regarding energy minimization. Suppose, I minimize the the protein solvated in water, the energy value that I get is for the whole system or for the protein alone. If it's for the system then how can I get the energy for the protein alone. You can define energy groups (see manual) to do this for the nonbonded contributions. Bonded contributions are easy to do in your case. Whether this energy is useful for anything is quite another matter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Dihedral Constraints
Thanks Sir for the reply... This question is related to my first query that if we constraint the dihedral of the turn residue how can we fix/freeze the movement of other residues. As I am interested in only getting the energy of the hairpin when the turn residues are constrained within a particular phi psi angle range On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 12:04 PM, bharat gupta wrote: Thanks for the reply . Is it possible to calculate the dihedral energy of certain residues, like in my case for turn residues ??.. How can that be done First, seek to define dihedral energy... Force fields are not parametrized such that parts of them are expected to correlate with observables. This another question is regarding energy minimization. Suppose, I minimize the the protein solvated in water, the energy value that I get is for the whole system or for the protein alone. If it's for the system then how can I get the energy for the protein alone. You can define energy groups (see manual) to do this for the nonbonded contributions. Bonded contributions are easy to do in your case. Whether this energy is useful for anything is quite another matter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Dihedral Constraints
I am not going to compare this with anything , I have to look for sequences and their corresponding energies and select the lowest scoring ones. I request you to kindly elaborate on freezing some portion of the protein. ( I am bit confused as in my case I am fixing the dihedral of turn residues which means constraining them simultaneously I want to freeze the other region of the protein. ) On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 4:38 PM, bharat gupta wrote: Thanks Sir for the reply... This question is related to my first query that if we constraint the dihedral of the turn residue how can we fix/freeze the movement of other residues. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints As I am interested in only getting the energy of the hairpin when the turn residues are constrained within a particular phi psi angle range .. and with what are you going to compare those energies? And what will that comparison mean? Mark On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 12:04 PM, bharat gupta wrote: Thanks for the reply . Is it possible to calculate the dihedral energy of certain residues, like in my case for turn residues ??.. How can that be done First, seek to define dihedral energy... Force fields are not parametrized such that parts of them are expected to correlate with observables. This another question is regarding energy minimization. Suppose, I minimize the the protein solvated in water, the energy value that I get is for the whole system or for the protein alone. If it's for the system then how can I get the energy for the protein alone. You can define energy groups (see manual) to do this for the nonbonded contributions. Bonded contributions are easy to do in your case. Whether this energy is useful for anything is quite another matter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Dihedral Constraints
Sorry for the last reply, I wrote turns with different sequences wrongly, it's actually the turn with different dihedral constraints. I searched the gromacs user list , where I found this link , regarding calculation of dihedral energy of selected residues. I want to know whether this method would be useful ?? On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 4:57 PM, bharat gupta wrote: I am not going to compare this with anything , I have to look for sequences and their corresponding energies and select the lowest scoring ones. You can't compare total energies of different sequences and get a meaningful answer. What's the difference in energy between an apple and an orange mean? You can compare the average energy of an apple cut into pieces with the average energy of a whole apple, but that doesn't necessarily relate to the same quantity measured for an orange, either. There's a lot of work in measuring a decent *free* energy difference between some states. I request you to kindly elaborate on freezing some portion of the protein. ( I am bit confused as in my case I am fixing the dihedral of turn residues which means constraining them simultaneously I want to freeze the other region of the protein. ) You need to read the link I gave last time and use constraints and restraints in the accepted GROMACS sense in order for people to be able to understand your meaning clearly. There are links there to the kind of methods that are available. I think you need to do some reading and thinking about those :-) If you lock down all the degrees of freedom then you can't measure anything relevant. Mark On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 4:38 PM, bharat gupta wrote: Thanks Sir for the reply... This question is related to my first query that if we constraint the dihedral of the turn residue how can we fix/freeze the movement of other residues. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints As I am interested in only getting the energy of the hairpin when the turn residues are constrained within a particular phi psi angle range .. and with what are you going to compare those energies? And what will that comparison mean? Mark On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/06/2012 12:04 PM, bharat gupta wrote: Thanks for the reply . Is it possible to calculate the dihedral energy of certain residues, like in my case for turn residues ??.. How can that be done First, seek to define dihedral energy... Force fields are not parametrized such that parts of them are expected to correlate with observables. This another question is regarding energy minimization. Suppose, I minimize the the protein solvated in water, the energy value that I get is for the whole system or for the protein alone. If it's for the system then how can I get the energy for the protein alone. You can define energy groups (see manual) to do this for the nonbonded contributions. Bonded contributions are easy to do in your case. Whether this energy is useful for anything is quite another matter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users
[gmx-users] Re: Dihedral Constraints
Hi, I wanted to simulate a beta-hairpin but with the dihedral angle of the turn residues constrained as per my wish for eg phi angle should not 60 and psi should be 90. Can anybody tell me how can I do this ?? Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Dihedral Constraints
Thanks for the reply . Is it possible to calculate the dihedral energy of certain residues, like in my case for turn residues ??.. How can that be done This another question is regarding energy minimization. Suppose, I minimize the the protein solvated in water, the energy value that I get is for the whole system or for the protein alone. If it's for the system then how can I get the energy for the protein alone. On Thu, Jun 14, 2012 at 10:48 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/13/12 9:44 PM, bharat gupta wrote: Hi, I wanted to simulate a beta-hairpin but with the dihedral angle of the turn residues constrained as per my wish for eg phi angle should not 60 and psi should be 90. Can anybody tell me how can I do this ?? http://www.gromacs.org/**Documentation/How-tos/**Dihedral_Restraintshttp://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MPI installation
Hi, I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5. But while executing the command make mdrun , I am getting the following errorn:- mv -f .deps/xlate.Tpo .deps/xlate.Plo /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined -version-info 6:0:0 -o libgmxpreprocess_mpi.la -rpath /usr/local/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error 1 make[1]: Leaving directory `/usr/local/gromacs-4.5.5/src/kernel' I used this command to configure , before issuing make mdrun : ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3. Also I have mpich2 installed in my system. So, what could be reason for this error ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
Yes , I am using the correct options for dssp. But still I am getting the same error. On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
*This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp bash: /usr/local/bin/dssp: Permission denied I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? * On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: do_dssp
Ok now after downloading the latest version of dssp, and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :- [root@BHARATPC peptide2]# /usr/local/bin/dssp DSSP options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output -d [ --debug ] argDebug level (for even more verbose output) Examples: To calculate the secondary structure for the file 1crn.pdb and write the result to a file called 1crn.dssp, you type: dssp.exe -i 1crn.pdb -o 1crn.dssp On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 5:16 PM, bharat gupta wrote: *This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp * Don't run as root except for installing software, unless you like rebuilding your computer from the ground up. *bash: /usr/local/bin/dssp: Permission denied * Possibly you didn't give execute permission on some file or other. This is not a GROMACS problem, but rather a problem with how you have done your dssp installation. Consult its documentation. * I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? * You have now reported testing a command different from the one you reported that you had instructed do_dssp to use. So it is hard for me to believe your assertion that you are following the advice in do_dssp -h correctly with a correct version of DSSP. Mark * * On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Many of them. Start by making sure you're following the advice of do_dssp -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Monitoring of Salt bridges during simulation Run
You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html On Thu, Apr 5, 2012 at 5:23 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbondhttp://manual.gromacs.org/online/g_hbond.htmlutillity to monitor Hbonds within selection. Is there any specified program for such task but with salt-bridges only ? Thanks for help, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: do_dssp
Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 /dev/null 2 /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: REMD tutorial
Hi, I am planning to carry out a REMD study on a 12 residue beta-hairpin peptide. I have read the gromacs tutorial for that . I have certain doubts regarding the tutorial :- 1. Step. 4 says that run short simulations to have an estimate of the exchange rate (can get a good estimate within ~100 ps) and modify the temperatures if it does not correspond to the wished exchange. Do I have to run short MD of 100 ps for each replica . I am not able to understand this step ?? 2. I have currently 24 processors available for REMD. The temperature range that I have obtained from tgenerator server has 69 different values (300K-600K). I want to know how to calculate the no. of processors required for carrying out REMD for a certain temperature range ?? Kindly clarify these doubts Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Chromophore residue patch in gromacs
Hi, I have been trying to attach the chromophore of GFP in charmm ff parameter files. The parameters have been obtained from a published article. After making the changes as per the documentation ( http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) , I am getting following error :- Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 51 The chromophore residue number is 66, I don't understand why there is an error for residue 51 . Please help me in rectifying this error .. Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD error
Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD error
Thanks for the advice I re-complied everything again with static libraries and the installation went fine. But while executing the following command I am again getting error :- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v Fatal error: The number of nodes (1) is not a multiple of the number of simulations (3) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- BioBeat is Not Available In Regular Shops (P.J. Meulenhoff) Halting program mdrun_mpi gcq#155: BioBeat is Not Available In Regular Shops (P.J. Meulenhoff) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 I am trying to simulate 5 replicas and I have 4 cpu . On Thu, Jan 12, 2012 at 1:37 PM, lina lina.lastn...@gmail.com wrote: On Thursday 12,January,2012 08:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can you run a normal md smoothly? try: mdrun_mpi mdrun -deffnm prefix_0 if it works, then some of your trajectories not sound. means system does not equilibrium well. Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD error
The command I used this time :- mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100 Here's the error that I got :- Fatal error: The number of nodes (1) is not a multiple of the number of simulations (5) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Look at these, my work-strong arms (P.J. Harvey) Halting program mdrun_mpi gcq#345: Look at these, my work-strong arms (P.J. Harvey) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 12/01/2012 5:45 PM, bharat gupta wrote: It says that The number of cores must be a multiple of the number of replicas (given with -multi, which must equal the number of .tprhttp://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_Filefiles i.e., 10 for the above general example using prefix_0.tpr through prefix_9.tpr) I gave the options -multi 5 . But still I am getting the same error. Can you please explain, why is it so. Do I need to have the same no. of cores as the no. of .tpr files ?? You can't be getting an identical error, the numbers are different now. If mdrun is reporting the number of nodes is 1, then you have not configured your MPI environment correctly so that it knows how many processors you have available. You will need to solve this by reading your MPI documentation. If you have only four processors, you will not be able to run efficient REMD on five replicas, even if you can work out how to get MPI to over-allocate MPI processes to your physical processors. Please copy and paste command line and error together, so that people who might help don't feel like they might be wasting their time guessing. They have other things to do. Your example input below did not produce your error below, because 20 != 3. Mark On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 12/01/2012 5:29 PM, bharat gupta wrote: Thanks for the advice I re-complied everything again with static libraries and the installation went fine. But while executing the following command I am again getting error :- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v Fatal error: The number of nodes (1) is not a multiple of the number of simulations (3) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- BioBeat is Not Available In Regular Shops (P.J. Meulenhoff) Halting program mdrun_mpi gcq#155: BioBeat is Not Available In Regular Shops (P.J. Meulenhoff) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 I am trying to simulate 5 replicas and I have 4 cpu . See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps point 2. You cannot simulate an arbitrary number of replicas on an arbitrary number of processors. Mark On Thu, Jan 12, 2012 at 1:37 PM, lina lina.lastn...@gmail.com wrote: On Thursday 12,January,2012 08:54 AM, bharat gupta wrote: Hi, I am trying to run a REMD of a peptide. But while executing the following command after nvt and npt equilibration , I am getting the following error:- mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot enable executable stack as shared object requires: Permission denied Can you run a normal md smoothly? try: mdrun_mpi mdrun -deffnm prefix_0 if it works, then some of your trajectories not sound. means system does not equilibrium well. Can anybody suggest me how could I rectify this error. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor
Re: [gmx-users] Re: Folding rate
Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server?? On Sat, Dec 31, 2011 at 11:36 AM, felmer...@uchile.cl felmer...@uchile.clwrote: Yeah sure. There are several methods to trick your peptide to fold, but often you loose the real kinetics by using them. I think a 230 residues protein is too big to study folding kinetics through MD (because of the folding kinetics, not the size of the system). With topology based potenitials (Go-like models) you surely can do it, but take into account the the core asumption there is that the energy landscape of your peptide is perfectly funneled to the native state, which is a very good approximation for small protein (like a 100 residues) but not so nice for bigger proteins. In fact, even small proteins have intermediate states which makes the energy landscape somehow rugged (the engrailed homeodomain, the trp repressor, etc). Besides that, it is not a trivial task to go from the reduced representation to real kinetic constants. Maybe if you are interested in comparison rather than absolute values you can be lucky with the Go-modeling. If that is the case maybe you should try the SMOG potential it is very fast. regards Mensaje original De: bharat.85.m...@gmail.com Fecha: 30-dic-2011 22:45 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] Re: Folding rate The protein that I am dealing with is a 230 amino acid protein. I have come across some methods that used reduced space model of protein such as CABS for locating the protein folding pathway. An another paper describes about using Go model together with Rigid body dynamics for finding protein folding pathway. On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl felmer...@uchile.cl wrote: I small thing to consider with that particular paper is that DE Shaw has a special machine (Anton) to do those calculations, so in principle it is not possible to reproduce them (in a reasonable amount of time) on a regular (super)computer. I think your best shot, if your protein is small enough, is to use accelerated MD mixed with some good old kramer's theory. See for example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581. In any case it seems to me like too much of an effort, in the end here you really rely in the accuracy of the forcefield. Regards Mensaje original De: jmda...@itqb.unl.pt Fecha: 30-dic-2011 21:40 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] Re: Folding rate As it was pointed out, the literature is vast on this subject. Moreover, calculating folding rates from simulations is not a trivial subject, and it relies on many assumptions (e.g. what is considered folded, that the sampling obtained is enough). Even for small peptides, enough sampling may mean several hundreds of microsseconds, something not accessible to everyone. For a very recent article on the subject, check out: Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding Proteins Fold, *Science* 334:517-520. http://dx.doi.org/10.1126/science.1208351 Regards, João On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi k...@chemistry.umass.eduwrote: As Justin pointed out, there is a vast literature on this topic, you need to ask yourself what you seek, and look at many review articles to find some reasonable starting points for you own needs and designs. Beyond that, it's a lot of hard work... On Dec 30, 2011, at 7:04 PM, bharat gupta wrote: Thanks for your advice... Could you please refer me some papers regarding this On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.eduwrote: No, there is no way to use such data to determine the folding rate of the intact protein. If you used a fragment approach you could potentially (read lots of papers on REMD) isolate nucleation sites, but minus the tertiary interaction scheme you could not tell a compelling story. Now, if you want to find nucleation sites and see if there are spatially proximal sites and simulate them together... You might begin to tell a story. Ken On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote: bharat gupta wrote: Thanks for your reply. I want to whether does it make any sense or is it possible to simulate fragments of proteins and find their folding rate and then correlate it to folding rate of whole protein ?? Simulating arbitrary parts of a protein may or may not produce any relevant information, likely the latter. Independently folding domains might be simulated in isolation
Re: [gmx-users] Re: Folding rate
Thanks for the reply. Since I need to study the effect of beta-hairpin turn design on protein folding . I thought that first unfolding and then refolding would give the change in folding time. As you told that to do such a task would require large computational power. Is there any other method in MDS that could be used ?? On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/01/2012 12:35 PM, bharat gupta wrote: Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Well, it can be done, but you probably don't have enough computer to fold a 230 residue protein at atomistic resolution (or maybe even coarse-grained). Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server?? There's a significant literature on these subjects. I suggest you read some of it. Short answer: pick the highest temperature according to the size of the largest barrier you expect to cross (good luck guessing that), have around 20% exchange acceptance, and be prepared to observe where the replica-flow bottle necks are and to iteratively refine you temperatures. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Folding rate
Thanks for your advice... Could you please refer me some papers regarding this On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.edu wrote: No, there is no way to use such data to determine the folding rate of the intact protein. If you used a fragment approach you could potentially (read lots of papers on REMD) isolate nucleation sites, but minus the tertiary interaction scheme you could not tell a compelling story. Now, if you want to find nucleation sites and see if there are spatially proximal sites and simulate them together... You might begin to tell a story. Ken On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote: bharat gupta wrote: Thanks for your reply. I want to whether does it make any sense or is it possible to simulate fragments of proteins and find their folding rate and then correlate it to folding rate of whole protein ?? Simulating arbitrary parts of a protein may or may not produce any relevant information, likely the latter. Independently folding domains might be simulated in isolation, but if there is a chance that the peptide sequences have any effect on neighboring residues or even more distal sites, you'll never produce anything useful. -Justin On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to know whether it's possible to calculate the folding rate of 20 residue peptide folding into a beta-hairpin using gromacs ?? Anything is possible ;) But seriously, there is existing literature on such topics, I suspect you can find methodology that will suit your needs. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support
Re: [gmx-users] Re: Folding rate
The protein that I am dealing with is a 230 amino acid protein. I have come across some methods that used reduced space model of protein such as CABS for locating the protein folding pathway. An another paper describes about using Go model together with Rigid body dynamics for finding protein folding pathway. On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl felmer...@uchile.clwrote: I small thing to consider with that particular paper is that DE Shaw has a special machine (Anton) to do those calculations, so in principle it is not possible to reproduce them (in a reasonable amount of time) on a regular (super)computer. I think your best shot, if your protein is small enough, is to use accelerated MD mixed with some good old kramer's theory. See for example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581. In any case it seems to me like too much of an effort, in the end here you really rely in the accuracy of the forcefield. Regards Mensaje original De: jmda...@itqb.unl.pt Fecha: 30-dic-2011 21:40 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] Re: Folding rate As it was pointed out, the literature is vast on this subject. Moreover, calculating folding rates from simulations is not a trivial subject, and it relies on many assumptions (e.g. what is considered folded, that the sampling obtained is enough). Even for small peptides, enough sampling may mean several hundreds of microsseconds, something not accessible to everyone. For a very recent article on the subject, check out: Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding Proteins Fold, *Science* 334:517-520. http://dx.doi.org/10.1126/science.1208351 Regards, João On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi k...@chemistry.umass.eduwrote: As Justin pointed out, there is a vast literature on this topic, you need to ask yourself what you seek, and look at many review articles to find some reasonable starting points for you own needs and designs. Beyond that, it's a lot of hard work... On Dec 30, 2011, at 7:04 PM, bharat gupta wrote: Thanks for your advice... Could you please refer me some papers regarding this On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.eduwrote: No, there is no way to use such data to determine the folding rate of the intact protein. If you used a fragment approach you could potentially (read lots of papers on REMD) isolate nucleation sites, but minus the tertiary interaction scheme you could not tell a compelling story. Now, if you want to find nucleation sites and see if there are spatially proximal sites and simulate them together... You might begin to tell a story. Ken On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote: bharat gupta wrote: Thanks for your reply. I want to whether does it make any sense or is it possible to simulate fragments of proteins and find their folding rate and then correlate it to folding rate of whole protein ?? Simulating arbitrary parts of a protein may or may not produce any relevant information, likely the latter. Independently folding domains might be simulated in isolation, but if there is a chance that the peptide sequences have any effect on neighboring residues or even more distal sites, you'll never produce anything useful. -Justin On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I want to know whether it's possible to calculate the folding rate of 20 residue peptide folding into a beta-hairpin using gromacs ?? Anything is possible ;) But seriously, there is existing literature on such topics, I suspect you can find methodology that will suit your needs. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular
Re: [gmx-users] Re: Looking for potential phosphate binding sites
Yes, the phosphate ion moves around the protein but I am not able to find out how many of them bind to my protein. How can that be done ?? On Thu, Dec 1, 2011 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Hi, Hi, I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion. Now I want to know where does the phosphate ion bind on the protein surface or distribution of phosphate ions on protein surface ?? .. can help me finding out this Have you watched the trajectory to see what happens? -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Looking for potential phosphate binding sites
Hi, Is there any way to get the averaged distributions of ions around the protein surface. On Thu, Dec 1, 2011 at 9:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Yes, the phosphate ion moves around the protein but I am not able to find out how many of them bind to my protein. How can that be done ?? You'll have to set a definition for what you consider to be binding. Is a transient contact binding? Does the interaction have to persist for some length of time to be considered? In any case, you can print a list of contacts that occur with g_dist -dist, or use more complex selection criteria and generate dynamic indices with g_select (see the help text for examples). -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Protein ligand simulation
Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Protein ligand simulation
Actually I check the file newbox.gro in VMD and I found that the phosphate ion instead of being docked to my protein lies somewhere far away from the protein. The docked complex was taken from autodock's docking result. So what could have wrong . I guess this could be the reason for the box being too large . On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-**MODEL,300K,BOX(M)=1.86206NM,**WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Protein ligand simulation
I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? On Fri, Dec 2, 2011 at 11:00 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually I check the file newbox.gro in VMD and I found that the phosphate ion instead of being docked to my protein lies somewhere far away from the protein. The docked complex was taken from autodock's docking result. So what could have wrong . I guess this could be the reason for the box being too large . Sounds like you chose Autodock's undocked complex where the protein and ligand are far apart, but that's more of an Autodock question rather than a Gromacs one. -Justin On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-__**MODEL,300K,BOX(M)=1.86206NM,__** WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] Re: Protein ligand simulation
Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80 -0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60 -0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60 -0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90 -0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93 -0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering
Re: [gmx-users] Re: Protein ligand simulation
Sorry to ask this , but what could be done as I don't understand how could have happened?? On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80-0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60-0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60-0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90-0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93-0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users
Re: [gmx-users] Re: Protein ligand simulation
Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. On Fri, Dec 2, 2011 at 11:44 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry to ask this , but what could be done as I don't understand how could have happened?? I'll assume that you processed your .pdb file with pdb2gmx to get the protein coordinates in .gro format, but I don't know how you added the ligand coordinates to the .gro file. If you did it by hand (i.e. copy/paste with a text editor), then you didn't preserve the required units. If you used some other program (i.e. editconf) and it did not perform as expected, that is a separate issue. Since I'm left to guess (you still haven't described exactly what you've done to construct the file), that's all I can offer. -Justin On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50-0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80-0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60-0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60-0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60-0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90-0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60-0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93-0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49-0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00-0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00-0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Re: [gmx-users] Re: Protein ligand simulation
Sorry I didn't understand . Can u brief it ?? On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Protein ligand simulation
I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? I already did: http://lists.gromacs.org/**pipermail/gmx-users/2011-**December/04.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Protein ligand simulation
Yes, but I took the coordinates for phosphate ion from some other pdb file and docked with my protein using autodock. Then I generated the parameter for the ion using swissparam. Then prepared the protein file using pdb2gmx and pasted the coordinates of docked ion from the docked file obtained from autodock. What Shall I do now ?? ... On Fri, Dec 2, 2011 at 1:35 PM, Dallas Warren dallas.war...@monash.eduwrote: One file you used had the coordinates in angstroms, the other in nanometers. ** ** You cannot have numbers with different units in the same coordinate file. Which is what you did. Hence why they are not in the locations you assumed they were. ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Friday, 2 December 2011 3:22 PM *To:* jalem...@vt.edu; Discussion list for GROMACS users *Subject:* Re: [gmx-users] Re: Protein ligand simulation ** ** I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? ** ** I already did: http://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com ** ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Looking for potential phosphate binding sites
Hi, Hi, I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion. Now I want to know where does the phosphate ion bind on the protein surface or distribution of phosphate ions on protein surface ?? .. can help me finding out this Regards -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Restarting a crashed run
Hi, I was running a simulation of 10ns which crashed in between at 1.7 ns due to power failure. I used the following command to restart the simulation form that point: mdrun -s topol.tpr -cpi state.cpt -append After checking the file md_0_1.log and others , I am getting data only for those 1.7ns . How can I retrieve the data for the other half of the simulation that I restarted ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Restarting a crashed run
Hi, I was running a simulation of 10ns which crashed in between at 1.7 ns due to power failure. I used the following command to restart the simulation form that point: mdrun -s topol.tpr -cpi state.cpt -append After checking the file md_0_1.log and others , I am getting data only for those 1.7ns . How can I retrieve the data for the other half of the simulation that I restarted ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: simulation of protein/water and phosphate ion
I repeated the nvt equilibration with 500 ps and it was successful , after confirming the temperature graph. But during npt simulation, I got the following error:- step 131500, will finish Thu Sep 29 01:54:20 2011imb F 2% step 131520: Water molecule starting at atom 6981 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.5.4 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Since there are large no. of water molecules after 6981 , it means that it is not happening because oh some interaction with phosphate ion. What shall be done to rectify this ?? On Wed, Sep 28, 2011 at 12:35 PM, Dallas Warren dallas.war...@monash.eduwrote: And where are these waters? Close to the phosphate ions? ** ** You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself. ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Wednesday, 28 September 2011 1:30 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Re: simulation of protein/water and phosphate ion** ** ** ** it's showing error that certain atoms cannot be settled and these atoms are of solvent molecules i.e. Water On Wednesday, September 28, 2011, Dallas Warren dallas.war...@monash.edu wrote: What is actually blowing up? The protein or the phosphate ions? Do the phosphate ions run OK by themselves in water? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Wednesday, 28 September 2011 12:48 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion Hi, I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got LINCS error around 300ps. It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment?? On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ?? http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818
[gmx-users] Re: simulation of protein/water and phosphate ion
HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ?? Regards -- Bharat Ph.D. Candidate -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: simulation of protein/water and phosphate ion
Hi, I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got LINCS error around 300ps. It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment?? On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ?? http://www.gromacs.org/**Documentation/Terminology/** Blowing_Up#Diagnosing_an_**Unstable_Systemhttp://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: simulation of protein/water and phosphate ion
it's showing error that certain atoms cannot be settled and these atoms are of solvent molecules i.e. Water On Wednesday, September 28, 2011, Dallas Warren dallas.war...@monash.edu wrote: What is actually blowing up? The protein or the phosphate ions? Do the phosphate ions run OK by themselves in water? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Wednesday, 28 September 2011 12:48 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion Hi, I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got LINCS error around 300ps. It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment?? On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ?? http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] converting psf file to gromacs .itp file
Hi, Is there any way to convert NAMD generated psf file to GROMACS .itp file as I have generated the parameters for my compound using NAMD.. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding ffG43a1p force field
Dear Sir, It will be of great help to send the force field. actually I want to know whether it was working fine for u or not ?? ... Pls send the file and if it's working fine then I think you can deposit it in User contributions in gromacs repository... On Thu, Jun 23, 2011 at 2:38 PM, Ramachandran G gtr...@gmail.com wrote: Why you are doing simulation without chromophore? Chromophore is important in GFP. If you want i can send you the forcefield which i am using for GFP. Rama On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi Sir, Actually I am doing the simulation without the chromophore. So, planarity does not matter to be .. On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G gtr...@gmail.com wrote: Hi Bharat, I used Amber force field, but still i am not statisfied with the parameters which i used because after some nanosecond simulation(1 -2 ns) the planarity of the sturcture changes. I tired changing the force constant but still not much successfull. If you got success please let me know. with regards, Rama On Wed, Jun 22, 2011 at 10:11 PM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to simulate a docked complex of my protein (GFP) with phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters for pTYR, so I want to know how good is this FF for simulating my system... As in the literature its mentioned that people have used CHARMM, AMBER, OPLS ff for simulation of GFP. So, using this will be a correct choice or not ... -- Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding ffG43a1p force field
ok sir.. On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G gtr...@gmail.com wrote: Hi, That is the problem. Yet i do not know whether it is working fine not.i have been working with that for nearly 9-10months but not satisfied yet. In the following mail i will cut and paste the force field parameters which you can use it with amber. If you have time please go ahead and modify according to your wish. Regards, Rama On Wed, Jun 22, 2011 at 11:27 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, It will be of great help to send the force field. actually I want to know whether it was working fine for u or not ?? ... Pls send the file and if it's working fine then I think you can deposit it in User contributions in gromacs repository... On Thu, Jun 23, 2011 at 2:38 PM, Ramachandran G gtr...@gmail.com wrote: Why you are doing simulation without chromophore? Chromophore is important in GFP. If you want i can send you the forcefield which i am using for GFP. Rama On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta bharat.85.m...@gmail.com wrote: Hi Sir, Actually I am doing the simulation without the chromophore. So, planarity does not matter to be .. On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G gtr...@gmail.comwrote: Hi Bharat, I used Amber force field, but still i am not statisfied with the parameters which i used because after some nanosecond simulation(1 -2 ns) the planarity of the sturcture changes. I tired changing the force constant but still not much successfull. If you got success please let me know. with regards, Rama On Wed, Jun 22, 2011 at 10:11 PM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to simulate a docked complex of my protein (GFP) with phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters for pTYR, so I want to know how good is this FF for simulating my system... As in the literature its mentioned that people have used CHARMM, AMBER, OPLS ff for simulation of GFP. So, using this will be a correct choice or not ... -- Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un
Re: [gmx-users] Regarding ffG43a1p force field
these are in continuity I mean for the ffbonded.itp file On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G gtr...@gmail.com wrote: more parameters - ffbonded.itp NBCT 10.1444294553.6 NBC10.1404334720.0 C CC 10.1407343088.0 CCCB 10.1474468608.0 CB H2 10.1076129960.25 to aminoacids.hdb 1 1 HE2 CE2 CZ CD2 1 1 HE1 CE1 CZ CD1 1 1 HD1 CD1 CG2 CE1 1 1 HD2 CD2 CG2 CE2 1 2 HH OH CZ CE1 1 1 HB2 CB2 CA2 CG2 1 2 HG1 OG1 CB1 CA1 1 1 H N CA1 C1 On Thu, Jun 23, 2011 at 12:18 AM, Ramachandran G gtr...@gmail.com wrote: For ffbonded.itp, i added the following. (you need to be carefull here since i cooked upto the force constants) C CCCBCA9 180.0 4.309 1 NBCCC O 9 180.0 4.309 1 ; NBCCCBCA9 180.0 4.309 1 NBCCCBH29 180.0 4.309 1 C CCCBH29 180.0 4.309 1 NBCCC NB9 180.0 4.0876 1 CTNBC CC9 180.0 4.0876 1 CTNBC O 9 180.0 4.0876 1 CBCCC NB9 180.0 4.0876 1 CBCCC O 9 180.0 4.0876 1 CCC NBCC9 180.0 4.7656 1 O C NBCC9 180.0 4.7656 1; CCNBCTC 9 180.0 4.1400 1; C NBCTC 9 180.0 4.1400 1 ; CTCTOHHO4 180.0 4.1400 1 ; OH CTCT CC9 0.0 4.1400 1 OH CTCT N 9 180.0 4.9162 1 ; added newly improper dihedrals CBCCCA H2 4 180.04.1840 2 CCNBCB C4 180.04.1840 2 CCCTNB NB 4 180.04.1840 2 CTN CC CT 4 144.64 3.1840 2 NBO CC C4 180.04.1840 2 NBCCCCT 4 180.04.1840 2 CACBCA CA 4 180.04.1840 2 CAHACA CA 4 180.04.1840 2 ; added to test N CT CH4 180.04.1840 2 On Thu, Jun 23, 2011 at 12:13 AM, Ramachandran G gtr...@gmail.comwrote: For the GFP chromophore i name residue as CRIH. 1. aminoacids.rtp CB2 CB 0.019103 1 CA2 CC-0.026635 2 N2 NB-0.436463 3 C1 CC 0.302706 4 N3 NB-0.541478 5 C2 C 0.563844 6 OC2 O -0.394118 7 CG2 CA-0.079330 8 CZ CA 0.240178 9 CD1 CA-0.072596 10 HD1 HA 0.129374 11 CD2 CA-0.070677 12 HD2 HA 0.091532 13 CE1 CA-0.129374 14 HE1 HA 0.091792 15 CE2 CA-0.087778 16 HE2 HA 0.112301 17 OH OH-0.454413 18 H H 0.37107 19 HH HO 0.258435 20 N N -0.61682 21 CA1 CT-0.116631 22 CB1 CT-0.03127 23 OG1 OH-0.74662 24 HG1 HO 0.45887 25 HB2 H2 0.116716 26 CA3 CT-0.250251 27 CC 0.35254 28 OO-0.48366 29 [ bonds ] C1 CA1 N3 CA3 N3 C1 N3 C2 C2 OC2 C1 N2 C2 CA2 N2 CA2 CA2 CB2 CB2 CG2 CG2 CD1 CG2 CD2 CD1 CE1 CD2 CE2 CE1 CZ CE2 CZ CZ OH CB1 OG1 OH HH CB2 HB2 CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 CA1 N CA1 CB1 CA3 C C O OG1 CB1 OG1 HG1 N H -C N +N C [ angles ] ; aiajak th0 cth ub0 cub N2 C1 N3 114.0 1087.87 C1N2 CA2 106.0 1087.87 C1N3 C2107.9 1087.87 N2CA2 C2108.3 1087.87 N2CA2 CB2 129.5 376.56 C2N3 CA3 123.4 267.776 N3C2 OC2 126.0 351.456 N3C2 CA2 103.0 1087.87 OC2 C2 CA2 132.0 317.984 C2CA2 CB2 122.0 376.56 CA2 CB2 CG2 130.0 1087.87 CB2 CG2 CD1 121.0 383.2544 CB2 CG2 CD2 121.0 383.2544 CG2 CD1 CE1 120.0 334.72 CG2 CD2
