[gmx-users] No Distribution?
Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 23 13 And I’m still getting the same error. Any insights? Thanks, Xu Huang -- 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] No Distribution?
@ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -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] No Distribution?
Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? On Nov 2, 2013, at 6:50 PM, Xu Dong Huang xudonghm...@gmail.com wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 123, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -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] No Distribution?
@ Justin, Thanks. I fixed the index files like you suggested. I’m getting logical results now. All the best, On Nov 2, 2013, at 7:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 7:01 PM, Xu Dong Huang wrote: Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? No. If you want three different distances, you need three groups, as I said in my previous message, and I even wrote the exact index file for you. -Justin On Nov 2, 2013, at 6:50 PM, Xu Dong Huang xudonghm...@gmail.com wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 123, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -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
[gmx-users] No group in index file?
Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Any insight can be appreciated Thanks, Xu Huang-- 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] No group in index file?
Dear all, so after I opened angle.ndx file in a text editor, the file appears to be blank. How can I properly make a index file since the command I issued seems to produce a blank index file? Is there something wrong with my input regarding npt.tpr? Thanks for your input, Xu Huang On Oct 31, 2013, at 1:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 1:36 PM, Xu Dong Huang wrote: Dear all. Since I am interested in finding the average angle, dihedrals in my system, I attempted to use g_angle, but then I realized I need to make index file using mk_angndx, I issued the following: mk_angndx -s npt.tpr -n angle.ndx and then i used g_angle -f not.xtc -n angle.ndx -ov angle.xvg -noperiodic -type angle and then I get the following error: Fatal error: Error: no groups in indexfile How can my index file not have the groups in there? How can I go about fixing this Inspect it with a text editor and/or gmxcheck. -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] No group in index file?
@ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 2, 23 and 13. How should I go about achieving that? Thanks, Xu Huang On Oct 31, 2013, at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 3:59 PM, Riccardo Concu wrote: Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx make_ndx is not particularly useful for angles. To get it to recapitulate the function of mk_angndx, it's as much work as writing the index file by hand. -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] No group in index file?
@ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. On Oct 31, 2013, at 4:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 4:22 PM, Xu Dong Huang wrote: @ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 2, 23 and 13. How should I go about achieving that? If you have 3 atoms/particles, there can be only one angle, by definition. Do you have an [angles] directive in the topology? That's how mk_angndx parses the .tpr file - by creating groups of similar angles based on theta and ktheta. If your model doesn't specify any angle potential, then mk_angndx will bail out and return nothing, though it should probably do that in a more elegant way than producing an empty file. -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] No group in index file?
@ Justin, Excellent advice. Thank you! And for the equilibrium angle, what is the approximate range I can define it to be? Say target is 90 degrees, should I define maybe 130 and let it oscillate? I guess question is how far is too far off? Thanks, On Oct 31, 2013, at 4:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 4:44 PM, Xu Dong Huang wrote: @ Justin, I did not define [angles] in the topology but I do have the angles result from All-atom run using OPLS forcefield. The reason for me not to include it in MARTINI forcefield topology is because I wanted to see if it will produce similar angle result of atom 12, 13 and 23 in martini water since the behavior of particle types I chose for my 3 atoms are well defined by martini at this point. My interest is to find for which force constant K value will the martini model match the all-atom model using OPLS. And you’re right, sorry, I got confused about the angles, there should only be 1. However, even the angle value I received doesn’t match the traditional all-atom result. What will happen if I define the [angles] part with the angles I received from traditional simulation? Because ultimately I am trying to find the k value parameter that will make the 3 particle display an angle similar to traditional run. If you define an equilibrium angle for 1-2-3, it will oscillate harmonically around that value, with the distribution determined by the value of k. I suspect that is how you can tune the parameters, by matching the distributions produced in the two simulations rather than a single target value, because with the angle defined in the topology, you're sort of predetermining the outcome. -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
[gmx-users] probability distribution of bond distance/length
Dear all, I would like to assess the probability distribution of particle bond distance/length over the entire run, specifically I want to collect possibly a histogram representation or even a regular plot. Would using g_bond be the correct way to obtain the probability distribution? Or is there another function that gets probability distribution specifically. Also, if using g_bond, it will give me an average (I suppose), so how can I get a histogram/data series representation? (I do not want to visualize this result using xmgrace) P.S I believe someone earlier suggested a link to the data collection reporting procedure, I tried it and changed the .xvg to a .csv, but the data reported in excel format all belongs to 1 single column, which won’t let me make a plot. Any insight is appreciated it. Xu Huang-- 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] Obtaining trajectory coordinates at all dt
Hello, I have couple objectives as part of an analysis of my simulated system. And I would like some opinions on the tools to use to achieve it. I have the following interest in my system: 1) Find the probability distribution (density) of bond angle on my molecule between (i.e atom 12, 2,3 , 13, etc) as a function of time step, essentially, the equilibrium angle. [would I use g_chi for such analysis? ] 2) I want the above result in an excel spreadsheet, is there a way to obtain it as a spreadsheet? Or I can only get a plot representation as a function of time? Please share your expertise and opinions. Thank you. Xu Huang -- 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] concenating cpt or not required?
Dear gromacs users, I just realized that even after trying to re-start a run, i still got separate name files (idk why), but I managed to combine err, xtc files, but don't know how to bring 2 .cpt files together, or is it not required? I'm trying to do NPT run next, and it will -t *.cpt, but I don't know if it matters that I don't have the 1st half, I only have the .cpt from restart run. Please let me know, thanks. -- 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] Restarting simulation -s. files?
Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? Thanks, Xu Huang Research Assistant Chemical Biochemical Engineering Rutgers School of Engineering -- 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] Restarting simulation -s. files?
Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? On Sep 28, 2013, at 2:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/13 2:46 PM, Xu Dong Huang wrote: Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? If you're getting files named -s.* as output, then what you typed above was not your command. Always copy and paste. Likely, your mdrun line was mdrun -deffnm -s ..., in which case, the .tpr file name is simply ignored and the file name prefix was set as -s, as your output would indicate. -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] Restarting simulation -s. files?
I see, Thank you for the information Justin. On Sep 28, 2013, at 2:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/13 2:52 PM, Xu Dong Huang wrote: Justin, I see. Is there a way to *stitch* the two files together so I can continue onto a NPT run? Appending is the default behavior of mdrun, if invoked properly and the files haven't been messed with. If not, trjcat appends trajectories and eneconv appends energy files. -Justin On Sep 28, 2013, at 2:49 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/13 2:46 PM, Xu Dong Huang wrote: Hello gromacs users, I restarted my run due to power failure using mdrun -v -s .tpr -cpi .cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make it so it continues to update the original .xtc and .tpr files? If you're getting files named -s.* as output, then what you typed above was not your command. Always copy and paste. Likely, your mdrun line was mdrun -deffnm -s ..., in which case, the .tpr file name is simply ignored and the file name prefix was set as -s, as your output would indicate. -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] do_dssp
Preeti, if do_dssp doesn't work for you, try to do it manually using the following web service: http://www.cmbi.ru.nl/hsspsoap/ I use it because my platform (MAC OSX) can't run DO_DSSP Best of luck! On May 14, 2013, at 11:00 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: I am facing problem while using do_dssp.I -- 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] Extending NPT run
Dear advanced users, I'm trying determine the procedure for extending NPT run (i.e I realized the NPT run I did wasn't long enough, so I wish to run it for another million steps. ) what should I do to set up the run again continuing with the previous data? Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] Extending NPT run
Thank you. I was just reading that as well, but didn't realize it could also be used to extend. I thought it was just runs that terminated early. Thanks Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 27, 2013, at 9:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/27/13 9:49 PM, Xu Dong Huang wrote: Dear advanced users, I'm trying determine the procedure for extending NPT run (i.e I realized the NPT run I did wasn't long enough, so I wish to run it for another million steps. ) what should I do to set up the run again continuing with the previous data? http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -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/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 -- 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] Extending NPT run
If I don't specify -extend (time) , will it automatically use the time step defined in the .tpr i'm using? Or should I just define the time anyway ? Thanks Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 27, 2013, at 9:54 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Thank you. I was just reading that as well, but didn't realize it could also be used to extend. I thought it was just runs that terminated early. Thanks Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 27, 2013, at 9:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/27/13 9:49 PM, Xu Dong Huang wrote: Dear advanced users, I'm trying determine the procedure for extending NPT run (i.e I realized the NPT run I did wasn't long enough, so I wish to run it for another million steps. ) what should I do to set up the run again continuing with the previous data? http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -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/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 -- 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] I can't figure out what is wrong with my .gro
Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where. Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg Thanks for any input. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] I can't figure out what is wrong with my .gro
@ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:07 PM, Xu Dong Huang wrote: Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where. Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg The last line of the .gro file (box vectors) does not end in a newline character. I discovered this by running: wc -l star.gro which returned 103, which would indicate that there should be 100 atoms in addition to a title line, number of atoms, and box vectors. Since there are 101 listed atoms, I knew there was a problem, likely with the last line. Adding a newline character allows the structure to be opened in VMD. -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/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 -- 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] I can't figure out what is wrong with my .gro
@ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -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/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 -- 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] I can't figure out what is wrong with my .gro
@Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -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/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 -- 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] I can't figure out what is wrong with my .gro
@Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -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/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 -- 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] I can't figure out what is wrong with my .gro
Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:58 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -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/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 -- 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
Re: [gmx-users] I can't figure out what is wrong with my .gro
Must be something wrong with my editor program (BBEdit), because when I open the file you sent me, it shows me there an additional blank line. Ok, time to switch to regular text editor… Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:04 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 8:02 PM, Xu Dong Huang wrote: Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line There is no additional line. The last line in the file must be the box vectors. -Justin Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:58 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did that, and it still says I have 103. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:49 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:22 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @ Justin, I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things. Thanks again, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/9/13 7:16 PM, Xu Dong Huang wrote: @ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? The thing you get when you press enter. http://en.wikipedia.org/wiki/Newline#In_programming_languages Note that Google has plenty more to say ;) There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character. So at the end of your box vector line, hit return then backspace. -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/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 -- 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 -- 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/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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org
[gmx-users] EM error
Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] EM error
Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] EM error
@ Justin, Thank you, that worked like a charm! (Using increased vanderwal distance) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:42 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD it's certainly not overlapping with my solute. ) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:12 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear users, Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= 14524 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = 4.4832208e+19 Maximum force =inf on atom 14524 Norm of force =inf gcq#182: That Was Cool (Beavis and Butthead) -My EM.mdp file contains the following: integrator = steep dt = 0.020 nsteps = 5 ;Note: 100 steps is to much for a vacuum run (nsteps=10) nstlog = 1000 nstenergy= 500 nstxtcout= 500 nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 epsilon_rf = 1 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 My system size 73191 W, and 1 star (consisted of 101 atoms) I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] after NVT run, molecule becomes dispersed/ loose
Dear users, I have a defined polymer .gro file and I ran energy minimization on it. However, when I attempt to run NVT on the polymer in a vacuum (box, no solvent), and I view the output .gro and trajectory in VMD, I see that my polymer is no longer a star, the beads are flying in every random direction, no beads are in bond connection as they should be. Any insight into why my polymer blew up in vacuum? (please let me know what kind of additional information you'd like to see) Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] after NVT run, molecule becomes dispersed/ loose
for some reason my message is too long and held for approval, but anyway, Starting Energy Minimized structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png Ending NVT outcome .gro structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83509PM_zpsb4f658b2.png @Justin, this is the same star polymer you've seen before, and I assume you were aware that there is a definite bond interaction definition and etc. (So I don't think the structure should have blown up like that) MDP information: integrator = md tinit= 0.0 dt = 0.02 nsteps = 10 nstcomm = 1 comm-grps= nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 The topology is the same one from last time I sent you, a star. bond order defined. (Can't attach it on here because it's too long and my message will be held for approval by gmx) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/5/13 8:29 PM, Xu Dong Huang wrote: Dear users, I have a defined polymer .gro file and I ran energy minimization on it. However, when I attempt to run NVT on the polymer in a vacuum (box, no solvent), and I view the output .gro and trajectory in VMD, I see that my polymer is no longer a star, the beads are flying in every random direction, no beads are in bond connection as they should be. Any insight into why my polymer blew up in vacuum? (please let me know what kind of additional information you'd like to see) At minimum, you need to post the contents of your topology and .mdp file. Without that information, no one can make any assessment of what's going on. Images of the starting and ending configurations can also be useful. -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/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 -- 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] after NVT run, molecule becomes dispersed/ loose
@Justin, actually. After a second thought and closer examination in VMD using RESTYPE differentiation, maybe this is the correct output because 95% of the beads shown are hydrophobic so they probably like to clump together after 10 time step …. I'm going to shorten my nstep in MD and see if I get a less clumped structure. Thank you Justin, and sorry for the impulsive question. I'll let you know if there is a further problem. Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:45 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: for some reason my message is too long and held for approval, but anyway, Starting Energy Minimized structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png Ending NVT outcome .gro structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83509PM_zpsb4f658b2.png @Justin, this is the same star polymer you've seen before, and I assume you were aware that there is a definite bond interaction definition and etc. (So I don't think the structure should have blown up like that) MDP information: integrator = md tinit= 0.0 dt = 0.02 nsteps = 10 nstcomm = 1 comm-grps = nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 The topology is the same one from last time I sent you, a star. bond order defined. (Can't attach it on here because it's too long and my message will be held for approval by gmx) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/5/13 8:29 PM, Xu Dong Huang wrote: Dear users, I have a defined polymer .gro file and I ran energy minimization on it. However, when I attempt to run NVT on the polymer in a vacuum (box, no solvent), and I view the output .gro and trajectory in VMD, I see that my polymer is no longer a star, the beads are flying in every random direction, no beads are in bond connection as they should be. Any insight into why my polymer blew up in vacuum? (please let me know what kind of additional information you'd like to see) At minimum, you need to post the contents of your topology and .mdp file. Without that information, no one can make any assessment of what's going on. Images of the starting and ending configurations can also be useful. -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/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 -- 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
Re: [gmx-users] after NVT run, molecule becomes dispersed/ loose
@Justin, Yeah I allowed the NVT to run for way too long. Therefore I get a super clumped structure. (Where as I only wanted a slightly clumped structure). I reduced the nsteps to about 3000 from 100 thousand to achieve my desired structure. Thanks for the support. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:51 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, actually. After a second thought and closer examination in VMD using RESTYPE differentiation, maybe this is the correct output because 95% of the beads shown are hydrophobic so they probably like to clump together after 10 time step …. I'm going to shorten my nstep in MD and see if I get a less clumped structure. Thank you Justin, and sorry for the impulsive question. I'll let you know if there is a further problem. Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:45 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: for some reason my message is too long and held for approval, but anyway, Starting Energy Minimized structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png Ending NVT outcome .gro structure: http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83509PM_zpsb4f658b2.png @Justin, this is the same star polymer you've seen before, and I assume you were aware that there is a definite bond interaction definition and etc. (So I don't think the structure should have blown up like that) MDP information: integrator = md tinit= 0.0 dt = 0.02 nsteps = 10 nstcomm = 1 comm-grps = nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 The topology is the same one from last time I sent you, a star. bond order defined. (Can't attach it on here because it's too long and my message will be held for approval by gmx) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 8:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/5/13 8:29 PM, Xu Dong Huang wrote: Dear users, I have a defined polymer .gro file and I ran energy minimization on it. However, when I attempt to run NVT on the polymer in a vacuum (box, no solvent), and I view the output .gro and trajectory in VMD, I see that my polymer is no longer a star, the beads are flying in every random direction, no beads are in bond connection as they should be. Any insight into why my polymer blew up in vacuum? (please let me know what kind of additional information you'd like to see) At minimum, you need to post the contents of your topology and .mdp file. Without that information, no one can make any assessment of what's going on. Images of the starting and ending configurations can also be useful. -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/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 -- gmx-users mailing
[gmx-users] g_gyrate
Dear gromac users, If I wish to measure the distance from 1 end of my polymer to the other end, would it be valid to use g_gyrate? Even so, does that report just the radius, hence the function name radius of gyration? Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] g_gyrate
@ Justin, Thank you. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 5, 2013, at 9:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/5/13 9:08 PM, Xu Dong Huang wrote: Dear gromac users, If I wish to measure the distance from 1 end of my polymer to the other end, would it be valid to use g_gyrate? Even so, does that report just the radius, hence the function name radius of gyration? g_polystat may be even more useful. -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/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 -- 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] Unusual processing time
Dear gromac users, I submitted my NPT run into a MPI cluster. The size of my run system is an 85x85x85 box filled with water solvent. and I set NPT steps to be 100 (1million) with dt 0.02. The log says It will finish sometime in mid or towards end of february. Is that normal for a NPT run of that size? Or am I just faced with slow technology. Or am I doing something wrong (I requested 6 cores for my run) Please let me know, thanks. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] Unusual processing time
Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 box system with water solvent + large multiple solutes. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 3, 2013, at 9:29 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, I submitted my NPT run into a MPI cluster. The size of my run system is an 85x85x85 box filled with water solvent. and I set NPT steps to be 100 (1million) with dt 0.02. The log says It will finish sometime in mid or towards end of february. Is that normal for a NPT run of that size? Or am I just faced with slow technology. Or am I doing something wrong (I requested 6 cores for my run) Please let me know, thanks. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] Unusual processing time
The average of all my variations contain about 802780 atoms. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 3, 2013, at 9:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/3/13 9:33 PM, Xu Dong Huang wrote: Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 box system with water solvent + large multiple solutes. Performance depends mostly on the number of atoms. You haven't provided that information, so it's hard to judge what you might expect. -Justin Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 3, 2013, at 9:29 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, I submitted my NPT run into a MPI cluster. The size of my run system is an 85x85x85 box filled with water solvent. and I set NPT steps to be 100 (1million) with dt 0.02. The log says It will finish sometime in mid or towards end of february. Is that normal for a NPT run of that size? Or am I just faced with slow technology. Or am I doing something wrong (I requested 6 cores for my run) Please let me know, thanks. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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. Research Scientist 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 -- 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 segmentation Fault
Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] MPI segmentation Fault
Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all that is) Thanks for any input, Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:08 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] MPI segmentation Fault
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run For NVT.mdp: integrator = md tinit= 0.0 dt = 0.02 nsteps = 1 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 For NPT.mdp integrator = md tinit= 0.0 dt = 0.02 nsteps = 100 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 5.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 OUTPUT log FOR NVT RUN: Writing checkpoint, step 9760 at Wed Jan 2 06:43:55 2013 Step Time Lambda 1 200.00.0 Writing checkpoint, step 1 at Wed Jan 2 06:56:58 2013 Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.27815e+03 -2.21982e+070.0e+00 -2.21969e+072.99756e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.91994e+07 -2.18426e+072.99676e+027.09077e+02 == ### == A V E R A G E S == ### == Statistics over 10001 steps using 1001 frames Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.33393e+03 -2.22049e+070.0e+00 -2.22036e+072.98604e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.92176e+07 -2.18431e+072.98524e+027.06152e+02 Total Virial (kJ/mol) -9.41186e+057.05498e+016.65566e+02 7.05612e+01 -9.40675e+05 -3.05521e+00 6.65543e+02 -3.06027e+00 -9.44794e+05 Pressure (bar) 7.05835e+02 -4.93053e-02 -2.47918e-01 -4.93095e-027.05573e+02 -4.79105e-03 -2.47909e-01 -4.78920e-037.07047e+02 Total Dipole (D) 0.0e+000.0e+000.0e+00 Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:20 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all
Re: [gmx-users] MPI segmentation Fault
@Justin, forgot to mention, yes the NVT was ran using MPI as well. (You're right, the MPI is not the issue, because I took the file off my cluster and attempted to run NPT on my personal computer, it reported same segmentation error, fault 11) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/2/13 3:20 PM, Xu Dong Huang wrote: Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all that is) There is no outside of a periodic cell, so this is a non-problem. Was the NVT run done in parallel? If it was, it eliminates a faulty MPI installation. If not, then that's an easily testable variable to determine the problem with NPT. You haven't posted any .mdp files, which is another variable in determining the viability of any simulation. -Justin Thanks for any input, Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:08 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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. Research Scientist 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 -- 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] MPI segmentation Fault
Dear Justin, I will try your suggestion to rerun it on Berendsen coupling and see if there is any further problems. The system indeed contain the star shaped structure I showed you earlier (running multiple versions, containing from 1, 5, 10, 15 and 20 stars in a solvent box), the solvent is just martini defined water system. The first 50 beads of all 4 arms has hydrophobic interaction with the Water solvent. and the last 5 remaining beads on all 4 arms are set to have extreme similar hydrophilic interaction with martini water bead. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:43 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: @Justin, forgot to mention, yes the NVT was ran using MPI as well. (You're right, the MPI is not the issue, because I took the file off my cluster and attempted to run NPT on my personal computer, it reported same segmentation error, fault 11) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/2/13 3:20 PM, Xu Dong Huang wrote: Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all that is) There is no outside of a periodic cell, so this is a non-problem. Was the NVT run done in parallel? If it was, it eliminates a faulty MPI installation. If not, then that's an easily testable variable to determine the problem with NPT. You haven't posted any .mdp files, which is another variable in determining the viability of any simulation. -Justin Thanks for any input, Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:08 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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. Research Scientist 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 -- 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] Linear CG beads, grompp doesn't work
Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] Linear CG beads, grompp doesn't work
Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1P3 O1 mon 1 0.00 2P3 O1 mon 2 0.00 3P3 O1 mon 3 0.00 4P3 O1 mon 4 0.00 5P3 O1 mon 5 0.00 6P3 O1 mon 6 0.00 7P3 O1 mon 7 0.00 8P3 O1 mon 8 0.00 9P3 O1 mon 9 0.00 ……. [ bonds ] 12 1 0.4317000 23 1 0.4317000 34 1 0.4317000 45 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -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/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 -- 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] Linear CG beads, grompp doesn't work
@Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:46 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear Justin, My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 1, 2013, at 10:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 10:33 PM, Xu Dong Huang wrote: Dear advanced gromac users, I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that? It's the angles that make the system unstable. One can use virtual sites to get around the issue. There is a trivial example in a tutorial I wrote: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials. You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly. [atoms] 1 P3 O1 mon 1 0.00 2 P3 O1 mon 2 0.00 3 P3 O1 mon 3 0.00 4 P3 O1 mon 4 0.00 5 P3 O1 mon 5 0.00 6 P3 O1 mon 6 0.00 7 P3 O1 mon 7 0.00 8 P3 O1 mon 8 0.00 9 P3 O1 mon 9 0.00 ……. [ bonds ] 1 2 1 0.4317000 2 3 1 0.4317000 3 4 1 0.4317000 4 5 1 0.4317000 …… However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr -it returns the error of: Fatal error: The largest charge group contains 200 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please let me know if there is a way to go around that. Thank you. Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme. -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/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 -- 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] editconf not centering, and it is cutting off my molecule
Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. Any input is appreciated. Thank you! Xu Dong Huang Chemical Biochemical Engineering-Undergraduate Researcher Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] editconf not centering, and it is cutting off my molecule
Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. editconf builds boxes from the coordinate origin so that there are never negative coordinates. It should be able to deal with those coordinates, equally shifted, which it appears they were. Can you provide images of what's going on? I don't clearly understand what's wrong. What do you mean by cut off? Nonexistent? Incorrectly placed? -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/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 -- 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] editconf not centering, and it is cutting off my molecule
Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1starO12 0.430 0.000 0.000 1starO13 0.860 0.000 0.000 1starO14 1.290 0.000 0.000 1starO15 1.720 0.000 0.000 1starO16 2.150 0.000 0.000 1starO17 2.580 0.000 0.000 1starO18 3.010 0.000 0.000 1starO19 3.440 0.000 0.000 1starO1 10 3.870 0.000 0.000 1starO1 11 4.300 0.000 0.000 1starO1 12 4.730 0.000 0.000 1starO1 13 5.160 0.000 0.000 1starO1 14 5.590 0.000 0.000 1starO1 15 6.020 0.000 0.000 1starO1 16 6.450 0.000 0.000 1starO1 17 6.880 0.000 0.000 1starO1 18 7.310 0.000 0.000 1starO1 19 7.740 0.000 0.000 1starO1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O1 11 16.221 11.921 16.195 1star O1 12 16.651 11.921 16.195 1star O1 13 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... Another reason why I think my .gro is valid is that when I editconf, it says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is valid? Please let me know, thank you. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:40 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695
Re: [gmx-users] editconf not centering, and it is cutting off my molecule
Ok I sent it. Let me know if you did not receive them. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1star O13 0.860 0.000 0.000 1star O14 1.290 0.000 0.000 1star O15 1.720 0.000 0.000 1star O16 2.150 0.000 0.000 1star O17 2.580 0.000 0.000 1star O18 3.010 0.000 0.000 1star O19 3.440 0.000 0.000 1star O1 10 3.870 0.000 0.000 1star O1 11 4.300 0.000 0.000 1star O1 12 4.730 0.000 0.000 1star O1 13 5.160 0.000 0.000 1star O1 14 5.590 0.000 0.000 1star O1 15 6.020 0.000 0.000 1star O1 16 6.450 0.000 0.000 1star O1 17 6.880 0.000 0.000 1star O1 18 7.310 0.000 0.000 1star O1 19 7.740 0.000 0.000 1star O1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O1 11 16.221 11.921 16.195 1star O1 12 16.651 11.921 16.195 1star O1 13 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... Another reason why I think my .gro is valid is that when I editconf, it says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is valid? Please let me know, thank you. Yes, those files should be fine. Can you send me the two coordinate files (off-list) so I can investigate what's going on? -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/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 -- 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] genbox -nmol, atoms removed
Dear Advanced Gromacs users, I'm trying to generate a solvated system with 1 solute (In my case 3). I do genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro -p polymer.top My polymer molecule contains 201 atoms. box size 45x45x45 and it generates a system with the following messages: Found 1 molecule type: W ( 1 atoms): 4259200 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box Neighborsearching with a cut-off of 0.315 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.315 Coulomb: 0.315 LJ: 0.315 System total charge: 0.000 Grid: 254 x 254 x 254 cells Successfully made neighbourlist nri = 1851, nrj = 1983 Checking Protein-Solvent overlap: tested 867 pairs, removed 277 atoms. Checking Solvent-Solvent overlap: tested 1100 pairs, removed 0 atoms. Added 4258923 molecules Generated solvent containing 4258923 atoms in 4258923 residues Writing generated configuration to star_solv.gro star polymer Output configuration contains 4259727 atoms in 4258971 residues Volume : 512000 (nm^3) Density: 2539.37 (g/l) Number of SOL molecules: 0 **My problem is, the output configuration contains unequal amount of atoms and residues, and when I do the subtraction, the difference is the exact amount of atom of my original polymer molecule. (I'm assuming genbox removed my molecule out of the box) -How can I prevent that from happening? So that I can put as many additional polymer in the solvated system as I want? Thanks, Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] genbox -nmol, atoms removed
Thank you very much. I got it sorted out by following your advice. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 10:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 9:41 PM, Xu Dong Huang wrote: Dear Advanced Gromacs users, I'm trying to generate a solvated system with 1 solute (In my case 3). I do genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro -p polymer.top My polymer molecule contains 201 atoms. box size 45x45x45 and it generates a system with the following messages: Found 1 molecule type: W ( 1 atoms): 4259200 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box Neighborsearching with a cut-off of 0.315 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.315 Coulomb: 0.315 LJ: 0.315 System total charge: 0.000 Grid: 254 x 254 x 254 cells Successfully made neighbourlist nri = 1851, nrj = 1983 Checking Protein-Solvent overlap: tested 867 pairs, removed 277 atoms. Checking Solvent-Solvent overlap: tested 1100 pairs, removed 0 atoms. Added 4258923 molecules Generated solvent containing 4258923 atoms in 4258923 residues Writing generated configuration to star_solv.gro star polymer Output configuration contains 4259727 atoms in 4258971 residues Volume : 512000 (nm^3) Density: 2539.37 (g/l) Number of SOL molecules: 0 **My problem is, the output configuration contains unequal amount of atoms and residues, and when I do the subtraction, the difference is the exact amount of atom of my original polymer molecule. (I'm assuming genbox removed my molecule out of the box) -How can I prevent that from happening? So that I can put as many additional polymer in the solvated system as I want? You're doing too much at once. Run the -ci -nmol options in one step, then solvate with -cs. You can also specify exact starting positions for each individual molecule with editconf -center, which may be a more foolproof solution for complex systems. As I recall, -ci has issues with multi-residue molecules, but perhaps that's an old issue and is no longer relevant. -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/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 -- 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
