Re: [gmx-users] g_clustsize output
On 2010-05-22 00.28, toma0...@umn.edu wrote: Hello, Thanks for the response. g_clustsize outputs two xpm files of the weighted and non-weighted cluster size vs time. Is there another way for me to get number of clusters vs cluster size? Not without programming, but since the information is there when the xpmp files are written that should not be too difficult. Thanks, Mike On May 20 2010, David van der Spoel wrote: On 2010-05-20 04.55, toma0...@umn.edu wrote: Hello, I have a system of dimers which spontaneously assemble into clusters. I would like to get a plot of the number of clusters of size s vs s. In looking at g_clustsize I am able to obtain the average number of clusters vs time, the average cluster size vs time and a histogram of the average number of molecules in a cluster of size s. Am I missing something? Is there a way for me to get the number of clusters of a particular size vs cluster size? Thanks, Mike Tomasini g_clustsize will make an xpm plot for this as well, IIRC it is called csize.xpm. You can turn it into eps using xpm2ps. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] list of published papers
On 2010-05-22 06.53, Mark Abraham wrote: http://www.gromacs.org/Documentation/Gromacs_papers - Original Message - From: milad ekramnia m.ekram...@ph.iut.ac.ir Date: Saturday, May 22, 2010 14:14 Subject: [gmx-users] list of published papers To: gmx-users@gromacs.org Dear Gromacs users I can remember up to one year ago oldwww.gromacs indexed a list of published papers which were based on gromacs platform . but now I can't find it anymore . Anyone knows whether the list is still on the server or it has been removed ? It was lost in the move to the new server. Maybe we'll make a new one one day, but if you can do literature search you can just search for the papers citing those original gromacs papers. regards -- Milad Ekramnia Physics Department Isfahan University of Technology -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] the output of do_dssp
Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend Structure @ s1 legend Coil @ s2 legend Bend 0514 1 --- My system is dimer and each peptide has 6 residue. And the number I choose to analyze is 1. Protein. Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] shake and settle
Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file? Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] shake and settle
- Original Message - From: subarna thakur thakur.suba...@yahoo.co.in Date: Saturday, May 22, 2010 19:23 Subject: [gmx-users] shake and settle To: gmx-users@gromacs.org --- | Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file? Subarna Thakur [ settles ] in your water .itp file chooses settle. You can choose LINCS or SHAKE in the .mdp file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] the output of do_dssp
Hsin-Lin wrote: Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend Structure @ s1 legend Coil @ s2 legend Bend 0514 1 --- My system is dimer and each peptide has 6 residue. Then you have a problem. Your output indicates 14 residues are in a random coil, so either you have more than 12 total residues, or something went wrong in the dssp calculation. And the number I choose to analyze is 1. Protein. Perhaps this is why you had a problem. Normally, choosing Protein would cause the calculation to hang, but maybe that is not the case any more. See here for the proper group to choose and the rationale: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? I'd question your results first...you don't have 12 residues in your calculation, otherwise your protein is 14/12 = 117% random coil! Also realize that (by default) the Structure term only includes alpha helix, beta strand, bend, and turn. Other structural elements are not included. That may or may not be what you want, depending on the structural elements of your protein. -Justin Hsin-Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] rerun trajectory does not match input file
Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 ( Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group 10 ( Prot-Masses) has 3848 elements Group 11 ( Non-Protein) has 33922 elements Group 12 ( LIG) has 35 elements Group 13 ( SOL) has 33807 elements Group 14 ( Na) has 46 elements Group 15 ( Cl) has 34 elements Group 16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? You can, but it won't fix anything. Your original .xtc file saved only the coordinates of the Protein and LIG (per your output options), but your .tpr file has all of these atoms, regardless of what you choose to save. You can, however, create a .tpr file that has a just these atoms by passing your original .tpr file to tpbconv, using a suitable index group. -Justin integrator = md nsteps = 5 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes gen_seed = 805087 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] rerun trajectory does not match input file
John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 (Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group10 ( Prot-Masses) has 3848 elements Group11 ( Non-Protein) has 33922 elements Group12 ( LIG) has35 elements Group13 ( SOL) has 33807 elements Group14 ( Na) has46 elements Group15 ( Cl) has34 elements Group16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? You can, but it won't fix anything. Your original .xtc file saved only the coordinates of the Protein and LIG (per your output options), but your .tpr file has all of these atoms, regardless of what you choose to save. You can, however, create a .tpr file that has a just these atoms by passing your original .tpr file to tpbconv, using a suitable index group. -Justin integrator = md nsteps = 5 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes gen_seed = 805087 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] rerun trajectory does not match input file
Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... 0 System : 37770 atoms 1 Protein : 3848 atoms 2 Protein-H : 1980 atoms 3 C-alpha : 244 atoms 4 Backbone: 732 atoms 5 MainChain : 974 atoms 6 MainChain+Cb: 1206 atoms 7 MainChain+H : 1198 atoms 8 SideChain : 2650 atoms 9 SideChain-H : 1006 atoms 10 Prot-Masses : 3848 atoms 11 Non-Protein : 33922 atoms 12 LIG :35 atoms 13 SOL : 33807 atoms 14 Na :46 atoms 15 Cl :34 atoms 16 Other : 33922 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 12 1 Copied index group 12 'LIG' Copied index group 1 'Protein' Merged two groups with AND: 35 3848 - 0 Group is empty 1 12 Copied index group 1 'Protein' Copied index group 12 'LIG' Merged two groups with AND: 3848 35 - 0 Group is empty On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 ( Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group 10 ( Prot-Masses) has 3848 elements Group 11 ( Non-Protein) has 33922 elements Group 12 ( LIG) has 35 elements Group 13 ( SOL) has 33807 elements Group 14 ( Na) has 46 elements Group 15 ( Cl) has 34 elements Group 16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? You can, but it won't fix anything. Your original .xtc file saved only the coordinates of the Protein and LIG (per your output options), but your .tpr file has all of these atoms, regardless of what you choose to save. You can, however, create a .tpr file that has a just these atoms by passing your original .tpr file to tpbconv, using a suitable index group. -Justin integrator = md nsteps = 5 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes gen_seed = 805087 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
Re: [gmx-users] rerun trajectory does not match input file
John Shultz wrote: Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... 0 System : 37770 atoms 1 Protein : 3848 atoms 2 Protein-H : 1980 atoms 3 C-alpha : 244 atoms 4 Backbone: 732 atoms 5 MainChain : 974 atoms 6 MainChain+Cb: 1206 atoms 7 MainChain+H : 1198 atoms 8 SideChain : 2650 atoms 9 SideChain-H : 1006 atoms 10 Prot-Masses : 3848 atoms 11 Non-Protein : 33922 atoms 12 LIG :35 atoms 13 SOL : 33807 atoms 14 Na :46 atoms 15 Cl :34 atoms 16 Other : 33922 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 12 1 Copied index group 12 'LIG' Copied index group 1 'Protein' Merged two groups with AND: 35 3848 - 0 Group is empty 1 12 Copied index group 1 'Protein' Copied index group 12 'LIG' Merged two groups with AND: 3848 35 - 0 Group is empty The use of tells make_ndx to write out a group that is the intersection of these two. If there are no overlaps, the group is empty. What you want is the or operator: 12 | 1 -Justin On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 (Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group10 ( Prot-Masses) has 3848 elements Group11 ( Non-Protein) has 33922 elements Group12 ( LIG) has35 elements Group13 ( SOL) has 33807 elements Group14 ( Na) has46 elements Group15 ( Cl) has34 elements Group16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? You can, but it won't fix anything. Your original .xtc file saved only the coordinates of the Protein and LIG (per your output options), but your .tpr file has all of these atoms, regardless of what you choose to save. You can, however, create a .tpr file that has a just these atoms by passing your original .tpr file to tpbconv, using a suitable index group. -Justin integrator = md nsteps = 5 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes gen_seed = 805087 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral
Re: [gmx-users] rerun trajectory does not match input file
Thanks Justin! On Sat, May 22, 2010 at 10:12 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... 0 System : 37770 atoms 1 Protein : 3848 atoms 2 Protein-H : 1980 atoms 3 C-alpha : 244 atoms 4 Backbone : 732 atoms 5 MainChain : 974 atoms 6 MainChain+Cb : 1206 atoms 7 MainChain+H : 1198 atoms 8 SideChain : 2650 atoms 9 SideChain-H : 1006 atoms 10 Prot-Masses : 3848 atoms 11 Non-Protein : 33922 atoms 12 LIG : 35 atoms 13 SOL : 33807 atoms 14 Na : 46 atoms 15 Cl : 34 atoms 16 Other : 33922 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 12 1 Copied index group 12 'LIG' Copied index group 1 'Protein' Merged two groups with AND: 35 3848 - 0 Group is empty 1 12 Copied index group 1 'Protein' Copied index group 12 'LIG' Merged two groups with AND: 3848 35 - 0 Group is empty The use of tells make_ndx to write out a group that is the intersection of these two. If there are no overlaps, the group is empty. What you want is the or operator: 12 | 1 -Justin On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 ( Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group 10 ( Prot-Masses) has 3848 elements Group 11 ( Non-Protein) has 33922 elements Group 12 ( LIG) has 35 elements Group 13 ( SOL) has 33807 elements Group 14 ( Na) has 46 elements Group 15 ( Cl) has 34 elements Group 16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp md_prev.cpt md.tpr md.trr md.xtc traj.trr Here is my mdp file, should I remove entries for xtc_grps and energygrps to avoid this issue? You can, but it won't fix anything. Your original .xtc file saved only the coordinates of the Protein and LIG (per your output options), but your .tpr file has all of these atoms, regardless of what you choose to save. You can, however, create a .tpr file that has a just these atoms by passing your original .tpr file to tpbconv, using a suitable index group. -Justin integrator = md nsteps = 5 dt = 0.002 nstvout = 5000 nstlog = 500 nstenergy = 250 nstxtcout = 5000 nstxout = 5000 xtc_grps = Protein LIG energygrps = Protein SOL constraints = all-bonds nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 Pcoupl = parrinello-rahman PcOupltype = isotropic tau_p = 0.5
[gmx-users] Re: OPLS-AA/L force field
Hi,Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is protonate -f drg.pdb -o drg.gro, this is without hydrogens atoms too.I think something is wrong, but I don't know what it is.In definition of protonate there is protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb. but I can't add hydrogens. What is my problem?Thanksyou zou wrote: Hi again, Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true? Yes, a coordinate file contains a structure. If it is true, when I used editconf -f drg.pdb -o drg.gro number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro? The underlying assumption when running any simulation is that you have developed the proper parameters for the ligand and that it has an appropriate structure. If you need additional hydrogens, the Gromacs protonate tool can generate an all-atom structure. -Justin Thanks, you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true? If you want to use x2top, the assumption is that the structure is already appropriate as is, that is it is properly protonated. The only tool that is smart enough to add force field-specific hydrogens is pdb2gmx. If you're using OPLS-AA, then you should have all hydrogens present, anyway. If that's true, then you can use editconf to create a .gro file (which is not absolutely necessary; Gromacs can handle .pdb files just fine). If you don't have all the appropriate atoms present in your molecule's structure, then you need to build a proper structure. -Justin Thank you again you zou wrote: Hi Justin, Thank you for your help, But when I run x2top command there is one error that is: Can not find forcefield for atom C1-1 with 2 bonds Can not find forcefield for atom C4-4 with 2 bonds ... g t; Program x2top, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 6 out of 24 atoms Not all of your atom types are described by ffoplsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File I don't know how can I adjust this error. I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topo logy. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for gt; drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you can build the topology by hand. No matter what you choose, you ne ed a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: OPLS-AA/L force field
you zou wrote: Hi, Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is protonate -f drg.pdb -o drg.gro, this is without hydrogens atoms too. I think something is wrong, but I don't know what it is.In definition of protonate there is protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb http://rocks5.vki.ac.be/gromacs/online/hdb.html. but I can't add hydrogens. What is my problem? Well, your command isn't correct. The protonate command takes (at minimum) the -s flag, not -f (which is optional, and context-dependent, if I recall). The other fact is that if a residue isn't listed in ffgmx2.hdb, it won't get protonated, but it is trivial to add new molecules into the .hdb file with the help of the manual. The syntax for .hdb entries is straightforward. -Justin Thanks you zou wrote: Hi again, Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true? Yes, a coordinate file contains a structure. If it is true, when I used editconf -f drg.pdb -o drg.gro number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro? The underlying assumption when running any simulation is that you have developed the proper parameters for the ligand and that it has an appropriate structure. If you need additional hydrogens, the Gromacs protonate tool can generate an all-atom structure. -Justin Thanks, you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true? If you want to use x2top, the assumption is that the structure is already appropriate as is, that is it is properly protonated. The only tool that is smart enough to add force field-specific hydrogens is pdb2gmx. If you're using OPLS-AA, then you should have all hydrogens present, anyway. If that's true, then you can use editconf to create a .gro file (which is not absolutely necessary; Gromacs can handle .pdb files just fine). If you don't have all the appropriate atoms present in your molecule's structure, then you need to build a proper structure. -Justin Thank you again you zou wrote: Hi Justin, Thank you for your help, But when I run x2top command there is one error that is: Can not find forcefield for atom C1-1 with 2 bonds Can not find forcefield for atom C4-4 with 2 bonds ... g t; Program x2top, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a f orcefield type for 6 out of 24 atoms Not all of your atom types are described by ffop lsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File I don't know how can I adjust this error. I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topo logy. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin br you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for gt; drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you c an build the topology by hand. No matter what you choose, you ne ed a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing
[gmx-users] xtc file
Dear experts, I am trying to exclude all nonbonded interaction on hexane molecule. 1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v output.mdrun_m 2-Can you please check exclsusions directive in top file. I have used also nrexcl 5 in molecule top. does this make sense given that I have defined all the possible exclusions in 19 lines. grompp em : *checking input for internal consistency... Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 5 bonded neighbours molecule type 'Hexane' processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat Making dummy/rest group for T-Coupling containing 2500 elements Making dummy/rest group for Acceleration containing 2500 elements Making dummy/rest group for Freeze containing 2500 elements Making dummy/rest group for Energy Mon. containing 2500 elements Making dummy/rest group for VCM containing 2500 elements Number of degrees of freedom in T-Coupling group rest is 5122.00 Making dummy/rest group for User1 containing 2500 elements Making dummy/rest group for User2 containing 2500 elements Making dummy/rest group for XTC containing 2500 elements Making dummy/rest group for Or. Res. Fit containing 2500 elements Making dummy/rest group for QMMM containing 2500 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... NOTE 1 [file em.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. writing run input file... There was 1 note Back Off! I just backed up Hexane-Stack125_em.tpr to ./#Hexane-Stack125_em.tpr.4# gcq#320: Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family? (Gogol Bordello) :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: processing topology... turning all bonds into constraints... Analysing residue names: There are: 125 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... This run will generate roughly 1 Mb of data output md_em: teepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 200 Step=0, Dmax= 1.0e-02 nm, Epot= -2.41657e+03 Fmax= 1.96636e+02, atom= 1189 writing lowest energy coordinates. Back Off! I just backed up Hexane-Stack125_b4pr.gro to ./#Hexane-Stack125_b4pr.gro.4# Steepest Descents converged to Fmax 1000 in 1 steps Potential Energy = -2.41656779590808e+03 Maximum force = 1.96635853696765e+02 on atom 1189 Norm of force = 1.37247833599652e+02 **out put grompp md Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 5 bonded
Re: [gmx-users] xtc file
Moeed wrote: Dear experts, I am trying to exclude all nonbonded interaction on hexane molecule. 1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v output.mdrun_m As I think I have said several times, you have to do this in several steps. First, run a simulation using normal exclusions that you believe to be valid by evaluating the properties of the system. If you set nstxtcout 0 in your .mdp file, you will get a .xtc trajectory file (.xtc output is off by default - you must specify that you want it). After you have done this, use mdrun -rerun on this trajectory and whatever modified topology you have created. More specifically: 1. mdrun -deffnm md_no_excl 2. grompp to create new .tpr file with special exclusions 3. mdrun -rerun md_no_excl.xtc -s md_with_new_excl.tpr Thus, new energies will be calculated from a sensible trajectory. 2-Can you please check exclsusions directive in top file. I have used also nrexcl 5 in molecule top. does this make sense given that I have defined all the possible exclusions in 19 lines. Much of what you have defined is redundant. If you have nrexcl = 5 that means nonbonded interactions between atoms up to 5 bonds away are excluded already, so lines like 19 20 are unnecessary. snip All of the information I deleted is unnecessary. I appreciate that you are trying to be thorough, but long emails with excess detail dilute the information that is really needed. [ moleculetype ] ; Namenrexcl Hexane 5 Not a bad approach, but... [ exclusions ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 7 8 9 10 11 12 13 14 15 16 17 18 19 20 8 9 10 11 12 13 14 15 16 17 18 19 20 9 10 11 12 13 14 15 16 17 18 19 20 10 11 12 13 14 15 16 17 18 19 20 11 12 13 14 15 16 17 18 19 20 12 13 14 15 16 17 18 19 20 13 14 15 16 17 18 19 20 14 15 16 17 18 19 20 15 16 17 18 19 20 16 17 18 19 20 17 18 19 20 18 19 20 19 20 ...why all the redundancy? Much of what you have here is already encompassed by the value of nrexcl. Actually, if you set nrexcl = 7, you don't have to create an [exclusions] section at all! There are no atoms more than 7 bonds away from each other in hexane, right? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
