[gmx-users] Bond Energies Absent
Hi All, My edr files don't contain bond energies. Is there any reason apparent in this parameter file? ntegrator = md nsteps = 1000 dt = 0.002 nstvout = 100 nstlog = 500 nstenergy = 250 nstxtcout = 100 nstxout = 100 energygrps = Protein_LIG 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 tau_t = 0.1 tc-grps = Protein_LIG ref_t = 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 = 671928 -- 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] Merge Trajectories
Hi GMX Users, I am trying to merge some trajectories. Some of the trajectories are not matching correctly. There is a discrepancy in the number of atoms. Is there a way to report on the atom count for all these trajectories so I can know which ones to exclude? trjcat -f */*.xtc --- Program trjcat, VERSION 4.0.5 Source code file: gmx_trjcat.c, line: 100 Fatal error: Different numbers of atoms (3884/3907) in files -- 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] tpbconv subset
I modified the .mdp file, created a full system tpr, then ran it through tpbconv, then ran mdrun using the original xtc. It says the atom numbers don't match. mdrun -rerun md.xtc -v -s lig.tpr --- Program mdrun, VERSION 4.0.5 Source code file: md.c, line: 859 Fatal error: Number of atoms in trajectory (37655) does not match the run input file (65) --- On Sun, May 23, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? Modify the .mdp file the way you need to, create a full-system .tpr file, then run it through tpbconv. -Justin On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backwards. You don't need it. Assuming you want to do some sort of re-run procedure, you simply have to run: mdrun -s subset.tpr -rerun original.xtc (where original.xtc is your trajectory file that contains the same subset of atoms as subset.tpr) -Justin http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- 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
[gmx-users] tpbconv subset
I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- 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] tpbconv subset
Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backwards. You don't need it. Assuming you want to do some sort of re-run procedure, you simply have to run: mdrun -s subset.tpr -rerun original.xtc (where original.xtc is your trajectory file that contains the same subset of atoms as subset.tpr) -Justin http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- 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
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
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) 231
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
Re: [gmx-users] rerun trajectory does not match input file
Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me 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 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] g_dist output
I tried using the xtc instead but it says the atom range is outside the index g_dist -f md.xtc -s md.tpr -n index.ndx protein_lig.txt :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 4.0.5 (-: 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. :-) g_dist (-: Option Filename Type Description -f md.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s md.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt! Index file -o dist.xvg Output, Opt. xvgr/xmgr file -lt lifetime.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -distreal 0 Print all atoms in group 2 closer than dist to the center of mass of group 1 Reading file md.tpr, VERSION 4.0.5 (single precision) Group 0 ( System) has 38210 elements Group 1 ( Protein) has 3868 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 2670 elements Group 9 ( SideChain-H) has 1006 elements Group10 ( Prot-Masses) has 3868 elements Group11 ( Non-Protein) has 34342 elements Group12 ( LIG) has46 elements Group13 ( SOL) has 34212 elements Group14 ( Na) has48 elements Group15 ( Cl) has36 elements Group16 ( Other) has 34342 elements Select a group: Selected 1: 'Protein' Select a group: Selected 12: 'LIG' Reading frame 0 time0.000 --- Program g_dist, VERSION 4.0.5 Source code file: gmx_dist.c, line: 165 Fatal error: Atom number 3914 in an index group is larger than number of atoms in the trajectory (3868) --- Shaken, not Stirred (J. Bond) On Tue, Mar 9, 2010 at 9:03 AM, John Shultz jackygraha...@gmail.com wrote: Here is what our script is doing. It looks to me like we are analyzing the tpr when we should be checking the xtc or trr if I understand you correctly. And if we look at the trajectory we can measure the drift for the entire simulation rather than a specific instance. make_ndx -f md.tpr make_ndx.txt :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.0.5 (-: 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. :-) make_ndx (-: Option Filename Type Description -f md.tpr Input, Opt! Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt., Mult. Index file -o index.ndx Output Index file Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -natoms int 0 set number of atoms (default: read from
[gmx-users] g_dist output
Hello, I am seeking clarification on what this output means. I believe it says that the x axis is divided into 4 time intervals and they are plotted against a y axis that measures total distance along all 3 dimensional coordinates. Am I reading this correctly? # This file was created Sat Jan 30 00:20:03 2010 # by the following command: # g_dist -f md.gro -s md.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # Glycine aRginine prOline Methionine Alanine Cystine Serine # @title Distance @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.0000.06194480.05833030.0099401 -0.0183282 -- Jack -- 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] g_dist output
Print all atoms in group 2 closer than dist to the center of mass of group 1 Reading file md.tpr, VERSION 4.0.5 (single precision) Group 0 ( System) has 38210 elements Group 1 ( Protein) has 3868 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 2670 elements Group 9 ( SideChain-H) has 1006 elements Group10 ( Prot-Masses) has 3868 elements Group11 ( Non-Protein) has 34342 elements Group12 ( LIG) has46 elements Group13 ( SOL) has 34212 elements Group14 ( Na) has48 elements Group15 ( Cl) has36 elements Group16 ( Other) has 34342 elements Select a group: Selected 1: 'Protein' Select a group: Selected 12: 'LIG' Reading frames from gro file 'Protein in water', 38210 atoms. Last frame 0 time0.000 gcq#89: This Doesn't Suck, It's a Black Hole ! (K.A. Feenstra) # This file was created Tue Mar 9 13:58:58 2010 # by the following command: # g_dist -f md.gro -s md.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title Distance @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.0000.1572016 -0.1153002 -0.0301313 -0.1025198 On Tue, Mar 9, 2010 at 8:46 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: How come time is always 0.000 You're analyzing a .gro file, so there is no time information stored. If you analyze a trajectory (i.e., .xtc or .trr), then the time is saved in the individual frames. -Justin On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Hello, I am seeking clarification on what this output means. I believe it says that the x axis is divided into 4 time intervals and they are plotted against a y axis that measures total distance along all 3 dimensional coordinates. Am I reading this correctly? There should be no decomposition of time intervals here. Distance is plotted continuously as a function of time. The first column is time, then the total distance, then each of the x, y, and z components of that distance. -Justin # This file was created Sat Jan 30 00:20:03 2010 # by the following command: # g_dist -f md.gro -s md.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # Glycine aRginine prOline Methionine Alanine Cystine Serine # @ title Distance @ xaxis label Time (ps) @ yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.000 0.0619448 0.0583303 0.0099401 -0.0183282 -- 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 -- John Shultz 202-494-1707 -- 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
Re: [gmx-users] g_dist output
Thank you Justin. The LIG was missing from our default mdp parameters. That explains why we could not use the xtc file. I am adding it now. On Tue, Mar 9, 2010 at 9:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I tried using the xtc instead but it says the atom range is outside the index Well, 3868 is the number of atoms in your protein, so I'm guessing you set xtc_grps = Protein in the .mdp file. If you want to analyze other groups, then you have to actually save their coordinates when running your MD. -Justin g_dist -f md.xtc -s md.tpr -n index.ndx protein_lig.txt :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 4.0.5 (-: 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. :-) g_dist (-: Option Filename Type Description -f md.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s md.tpr Input Run input file: tpr tpb tpa -n index.ndx Input, Opt! Index file -o dist.xvg Output, Opt. xvgr/xmgr file -lt lifetime.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -dist real 0 Print all atoms in group 2 closer than dist to the center of mass of group 1 Reading file md.tpr, VERSION 4.0.5 (single precision) Group 0 ( System) has 38210 elements Group 1 ( Protein) has 3868 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 2670 elements Group 9 ( SideChain-H) has 1006 elements Group 10 ( Prot-Masses) has 3868 elements Group 11 ( Non-Protein) has 34342 elements Group 12 ( LIG) has 46 elements Group 13 ( SOL) has 34212 elements Group 14 ( Na) has 48 elements Group 15 ( Cl) has 36 elements Group 16 ( Other) has 34342 elements Select a group: Selected 1: 'Protein' Select a group: Selected 12: 'LIG' Reading frame 0 time 0.000 --- Program g_dist, VERSION 4.0.5 Source code file: gmx_dist.c, line: 165 Fatal error: Atom number 3914 in an index group is larger than number of atoms in the trajectory (3868) --- Shaken, not Stirred (J. Bond) On Tue, Mar 9, 2010 at 9:03 AM, John Shultz jackygraha...@gmail.com wrote: Here is what our script is doing. It looks to me like we are analyzing the tpr when we should be checking the xtc or trr if I understand you correctly. And if we look at the trajectory we can measure the drift for the entire simulation rather than a specific instance. make_ndx -f md.tpr make_ndx.txt :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.0.5 (-: 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. :-) make_ndx (-: Option Filename Type Description
Re: [gmx-users] g_dist output
How come time is always 0.000 On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: Hello, I am seeking clarification on what this output means. I believe it says that the x axis is divided into 4 time intervals and they are plotted against a y axis that measures total distance along all 3 dimensional coordinates. Am I reading this correctly? There should be no decomposition of time intervals here. Distance is plotted continuously as a function of time. The first column is time, then the total distance, then each of the x, y, and z components of that distance. -Justin # This file was created Sat Jan 30 00:20:03 2010 # by the following command: # g_dist -f md.gro -s md.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # Glycine aRginine prOline Methionine Alanine Cystine Serine # @ title Distance @ xaxis label Time (ps) @ yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.000 0.0619448 0.0583303 0.0099401 -0.0183282 -- 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 -- John Shultz 202-494-1707 -- 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
