Re: [gmx-users] Exploding poly-serine
Warren Gallin wrote: David, That is probably it, I had a 2-femtosecond step and no bond constraints. Obviously I need to read up on the pros and cons of the various restraint regimes. I guess that would be consistent with the sudden explosion after along period of stable running. Why poly-Ser would be more susceptible to this than poly-Pro, poly-Asp or poly-Gly is not obvious to me, but I am sure that there is a reason out there somewhere. If this is the cause, the difference in numerical stability may well not be caused by the difference in the residue (i.e. the physical model) but in the initial conditions. 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] Exploding poly-serine
David, That is probably it, I had a 2-femtosecond step and no bond constraints. Obviously I need to read up on the pros and cons of the various restraint regimes. I guess that would be consistent with the sudden explosion after along period of stable running. Why poly-Ser would be more susceptible to this than poly-Pro, poly- Asp or poly-Gly is not obvious to me, but I am sure that there is a reason out there somewhere. Thanks, Warren Gallin On 26-Aug-09, at 10:48 AM, David van der Spoel wrote: [Details deleted] So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? What time step are you using? Since you are not using bond- constraints the time step should be on the order of 0.5 fs. Warren Gallin ___ 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 thewww 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 Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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 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] Exploding poly-serine
Warren Gallin wrote: Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form using TINKER, with neither end capped, then use pdb2gmx, editconv, genbox and genion to set the forcefield to OPLSAA/L, place it in a box of tip3p water, neutralized in a .096 M NaCl solution. I am trying to track down why this is occurring, and the first thing that seems suspicious is that the initial energy minimization run reaches convergence with a rather large force remaining on one of the atoms - the final statement from the EM run is: Steepest Descents converged to machine precision in 6793 steps, but did not reach the requested Fmax < 10. Potential Energy = -4.9731194e+05 Maximum force = 7.1219537e+02 on atom 111 Norm of force = 6.5289087e+00 So I am thinking that with a large initial force on the polymer the system might be unrecoverably unstable and this is propagating through the subsequent steps of relaxing the water and the actual MD run to pop up as an explosion. If I look at the run log for the MD run, everything seems stable until the last step, at which point the temperature shoots up and the serine polymer explodes. Here are the last four steps from the run log: Step Time Lambda 208200 416.400020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.75158e+031.25586e+027.62176e+00 -6.45482e+011.16773e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80001e+036.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77043e+04 -3.15843e+051.01418e+063.17587e+02 -2.87690e+02 Step Time Lambda 208300 416.600020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.04345e+041.96147e+021.55806e+01 -3.31126e+011.24787e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80413e+036.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77229e+04 -3.14815e+051.02114e+063.17663e+02 -2.94492e+02 Step Time Lambda 208400 416.800020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 7.10106e+032.06975e+021.21357e+01 -2.52705e+011.16229e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.85247e+036.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.58806e+04 -3.19943e+051.02333e+063.10133e+02 -2.90942e+02 Step Time Lambda 208500 417.20.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.30968e+044.27637e+021.17359e+01 -5.59373e+011.39477e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80067e+036.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.03323e+05 -2.76511e+051.07569e+064.22292e+022.94766e+02 So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? What time step are you using? Since you are not using bond-constraints the time step should be on the order of 0.5 fs. Warren Gallin ___ 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 thewww 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 Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgm
Re: [gmx-users] Exploding poly-serine
Warren Gallin wrote: Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form using TINKER, with neither end capped, then use pdb2gmx, editconv, genbox and genion to set the forcefield to OPLSAA/L, place it in a box of tip3p water, neutralized in a .096 M NaCl solution. I am trying to track down why this is occurring, and the first thing that seems suspicious is that the initial energy minimization run reaches convergence with a rather large force remaining on one of the atoms - the final statement from the EM run is: Steepest Descents converged to machine precision in 6793 steps, but did not reach the requested Fmax < 10. Potential Energy = -4.9731194e+05 Maximum force = 7.1219537e+02 on atom 111 Norm of force = 6.5289087e+00 So I am thinking that with a large initial force on the polymer the system might be unrecoverably unstable and this is propagating through the subsequent steps of relaxing the water and the actual MD run to pop up as an explosion. If I look at the run log for the MD run, everything seems stable until the last step, at which point the temperature shoots up and the serine polymer explodes. Here are the last four steps from the run log: Step Time Lambda 208200 416.400020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.75158e+031.25586e+027.62176e+00 -6.45482e+011.16773e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80001e+036.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77043e+04 -3.15843e+051.01418e+063.17587e+02 -2.87690e+02 Step Time Lambda 208300 416.600020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.04345e+041.96147e+021.55806e+01 -3.31126e+011.24787e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80413e+036.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77229e+04 -3.14815e+051.02114e+063.17663e+02 -2.94492e+02 Step Time Lambda 208400 416.800020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 7.10106e+032.06975e+021.21357e+01 -2.52705e+011.16229e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.85247e+036.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.58806e+04 -3.19943e+051.02333e+063.10133e+02 -2.90942e+02 Step Time Lambda 208500 417.20.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.30968e+044.27637e+021.17359e+01 -5.59373e+011.39477e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80067e+036.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.03323e+05 -2.76511e+051.07569e+064.22292e+022.94766e+02 So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? You'll have to describe your equilibration protocol in detail, including your .mdp file, because energy minimization alone is not enough. 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? Possibly. However, I routinely minimize my protein structures to Fmax < 1000 (usually they reach about 700-900 Fmax), and I've not had a problem. 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? See my response to #1. Thorough equilibration is required, but we don't know all what you've done. -Justin Warren Gallin ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. L
[gmx-users] Exploding poly-serine
Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form using TINKER, with neither end capped, then use pdb2gmx, editconv, genbox and genion to set the forcefield to OPLSAA/L, place it in a box of tip3p water, neutralized in a .096 M NaCl solution. I am trying to track down why this is occurring, and the first thing that seems suspicious is that the initial energy minimization run reaches convergence with a rather large force remaining on one of the atoms - the final statement from the EM run is: Steepest Descents converged to machine precision in 6793 steps, but did not reach the requested Fmax < 10. Potential Energy = -4.9731194e+05 Maximum force = 7.1219537e+02 on atom 111 Norm of force = 6.5289087e+00 So I am thinking that with a large initial force on the polymer the system might be unrecoverably unstable and this is propagating through the subsequent steps of relaxing the water and the actual MD run to pop up as an explosion. If I look at the run log for the MD run, everything seems stable until the last step, at which point the temperature shoots up and the serine polymer explodes. Here are the last four steps from the run log: Step Time Lambda 208200 416.400020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.75158e+031.25586e+027.62176e+00 -6.45482e+01 1.16773e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80001e+036.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77043e+04 -3.15843e+051.01418e+063.17587e+02 -2.87690e+02 Step Time Lambda 208300 416.600020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 1.04345e+041.96147e+021.55806e+01 -3.31126e+01 1.24787e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80413e+036.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.77229e+04 -3.14815e+051.02114e+063.17663e+02 -2.94492e+02 Step Time Lambda 208400 416.800020.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 7.10106e+032.06975e+021.21357e+01 -2.52705e+01 1.16229e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.85247e+036.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 7.58806e+04 -3.19943e+051.02333e+063.10133e+02 -2.90942e+02 Step Time Lambda 208500 417.20.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 2.30968e+044.27637e+021.17359e+01 -5.59373e+01 1.39477e+02 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.80067e+036.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05 Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) 1.03323e+05 -2.76511e+051.07569e+064.22292e+02 2.94766e+02 So my questions are: 1) Am I missing some obvious step in setting up a stable simulation? 2) Is it true that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? Warren Gallin ___ 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
