Re: [gmx-users] g_hbond and contact
To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik On Mar 5, 2013, at 5:20 AM, Kavyashree M wrote: I am sorry There is no 7ws Its a typographic error. What I wanted to ask was - I am comparing two simulations S1 and S2 for contacts at a given cut off I used g_mdmat and g_hbond to calculate it. g_hbond outputs: of -num and -hbn was considered. 1. -hbn output was analysed to calculate how many contacts each atom has from both S1 and S2. 2. -num output graph was compared from both S1 and S2. g_mdmat output: of -no was considered. 3. -no output was analysed from both S1 and S2 using the third column or the second Y value which gives total contacts of each atom. It was observed that 1 and 3 matched exactly giving the same number of contacts each atom has (in the whole simulations). indicating that the number of contacts each atom has was more in S2 than S1. But the graph from 2 indicated that the number of contacts (along the trajectory) in S1 was higher than S2. My doubt is: The number of contact per atom follows S2 S1 while number of contacts per time follows S1 S2. I am unclear as to what I have to conclude from this observations. - I used the same cutoff throughout. - There has not been any swapping of the trajectory while analysing. Thank you Kavya On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx - r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_*** *CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
Re: [gmx-users] g_hbond and contact
Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- 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_hbond and contact
On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? Yes. So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? That depends. If 'contact' means unique interactions and 'atom' means e.g. all atoms in in your system, then yes. Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- 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] g_hbond and contact
Thank you Sir. On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? Yes. So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? That depends. If 'contact' means unique interactions and 'atom' means e.g. all atoms in in your system, then yes. Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] g_hbond and contact
On 3/4/13 11:25 AM, Kavyashree M wrote: Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. These statements don't make any sense. How did you determine that the number of contacts in simulation 2 was greater than simulation 1, but then the .xvg files showed the opposite? The number of contacts come from the .xvg files? Perhaps you simply swapped your files during analysis. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? An index group is a list of atom numbers. The .xvg output is whatever you tell it to be, in this case, the number of contacts within the group selected. -Justin Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- 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
Re: [gmx-users] g_hbond and contact
Sir, From Index file which gives the unique contacts - First section the list of atoms I want to analyse [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] second section : the unique contacts of each atoms with others [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. I hope I am clear this time. Thank you kavya On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:25 AM, Kavyashree M wrote: Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. These statements don't make any sense. How did you determine that the number of contacts in simulation 2 was greater than simulation 1, but then the .xvg files showed the opposite? The number of contacts come from the .xvg files? Perhaps you simply swapped your files during analysis. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? An index group is a list of atom numbers. The .xvg output is whatever you tell it to be, in this case, the number of contacts within the group selected. -Justin Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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_hbond and contact
On 3/4/13 12:04 PM, Kavyashree M wrote: Sir, From Index file which gives the unique contacts - First section the list of atoms I want to analyse When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] second section : the unique contacts of each atoms with others You don't define contacts in an index group, you define atoms that may or may not make contacts with others. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. -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
Re: [gmx-users] g_hbond and contact
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- 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_hbond and contact
On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- 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
Re: [gmx-users] g_hbond and contact
I am sorry There is no 7ws Its a typographic error. What I wanted to ask was - I am comparing two simulations S1 and S2 for contacts at a given cut off I used g_mdmat and g_hbond to calculate it. g_hbond outputs: of -num and -hbn was considered. 1. -hbn output was analysed to calculate how many contacts each atom has from both S1 and S2. 2. -num output graph was compared from both S1 and S2. g_mdmat output: of -no was considered. 3. -no output was analysed from both S1 and S2 using the third column or the second Y value which gives total contacts of each atom. It was observed that 1 and 3 matched exactly giving the same number of contacts each atom has (in the whole simulations). indicating that the number of contacts each atom has was more in S2 than S1. But the graph from 2 indicated that the number of contacts (along the trajectory) in S1 was higher than S2. My doubt is: The number of contact per atom follows S2 S1 while number of contacts per time follows S1 S2. I am unclear as to what I have to conclude from this observations. - I used the same cutoff throughout. - There has not been any swapping of the trajectory while analysing. Thank you Kavya On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_*** *CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use
