Re: [gmx-users] Energy Conservation at the Beginning of a Production Run
Thank you all for the help! Introducing the h-bond constraints into the minimization as well, did reduce the magnitude of the initial jump to 10.1 kJ per mole in the first 0.0066 ps but did not remove the problem entirely. I am also using different coulombtype's in the minimization (Cut-off) and the production run (PME). Could this be causing the spike, and, is this bad practice? The minimization did not converge when I used coulombtype = PME. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Thursday, March 28, 2019 8:16:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production Run On 3/28/19 6:02 PM, Kruse, Luke E.(MU-Student) wrote: > In the production run I have constraints on h-bonds and I do not have any > constraints in the minimization. This would account for a sudden change in energy. At step 0, your H positions will immediately change. -Justin > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of David van > der Spoel > Sent: Thursday, March 28, 2019 4:50:38 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production > Run > > Den 2019-03-28 kl. 21:19, skrev Kruse, Luke E.(MU-Student): >> In the mdout.mdp file corresponding to this run I have the line >> >> ; Do not constrain the start configuration >> continuation = no >> >> >> Do I need to change this to yes? > Maybe, try a 100 step run where you save energies at each time step. Did > you change anything else between minimization and production, e.g. > constraint settings? >> >> The plot of energy vs time looks like an under damped response to a set >> point change in control theory - slight overshooting after the first few >> steps, then settling down to an average value nicely. This is what is >> leading me to believe that there is a large, non conservative force near the >> beginning that becomes smaller, and conservative. >> >> Time (ps) >> >> 0.00 -1851396.981075 >> 0.10 -1851388.994856 >> 0.20 -1851390.001591 >> 0.30 -1851389.436699 >> 0.40 -1851389.760231 >> 0.50 -1851389.726310 >> 0.60 -1851389.808428 >> 0.70 -1851389.907829 >> 0.80 -1851389.840644 >> 0.90 -1851389.967373 >> 1.00 -1851390.061502 >> 1.10 -1851390.057500 >> 1.20 -1851390.086172 >> 1.30 -1851390.042747 >> 1.40 -1851390.060210 >> 1.50 -1851389.998599 >> 1.60 -1851390.120319 >> 1.70 -1851390.141846 >> 1.80 -1851390.131003 >> 1.90 -1851390.170220 >> 2.00 -1851390.141617 >> 2.10 -1851390.135779 >> 2.20 -1851390.255565 >> 2.30 -1851390.153947 >> 2.40 -1851390.238681 >> 2.50 -1851390.144512 >> 2.60 -1851390.255200 >> 2.633000 -1851390.178012 >> >> >> ____________ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of David van >> der Spoel >> Sent: Thursday, March 28, 2019 3:10:05 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Energy Conservation at the Beginning of a >> Production Run >> >> Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student): >>> Hello gromacs users, >>> >>> >>> I am trying to simulate a peptide amphiphile with the CHARMM27 force field. >>> To do this I have had to specify an additional bond type and bond, angle, >>> dihedral, etc. parameters in the .itp files of the force field. Then, to >>> check if I had done this correctly, I minimized the system, and ran a >>> production run to generate an NVE ensemble, so that I could make sure the >>> system was conserving energy appropriately. After looking at the energy vs >>> time plot (produces with the gmx energy command), however, the system jumps >>> from an initial energy, up ~20 kJ per mole and then conserves energy for >>> the most part (slight drifting but seems tolerable relative to the initial >>> discontinuity). Is this discontinuity a normal happenstance or a result of >>> bad minimization? >>> >> Is that at step 0 in the simulation? >> >> Please check options like >> ; Do not constrain the start configuration >> continuation
Re: [gmx-users] Energy Conservation at the Beginning of a Production Run
In the production run I have constraints on h-bonds and I do not have any constraints in the minimization. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: Thursday, March 28, 2019 4:50:38 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production Run Den 2019-03-28 kl. 21:19, skrev Kruse, Luke E.(MU-Student): > In the mdout.mdp file corresponding to this run I have the line > > ; Do not constrain the start configuration > continuation = no > > > Do I need to change this to yes? Maybe, try a 100 step run where you save energies at each time step. Did you change anything else between minimization and production, e.g. constraint settings? > > > The plot of energy vs time looks like an under damped response to a set point > change in control theory - slight overshooting after the first few steps, > then settling down to an average value nicely. This is what is leading me to > believe that there is a large, non conservative force near the beginning that > becomes smaller, and conservative. > > Time (ps) > > 0.00 -1851396.981075 > 0.10 -1851388.994856 > 0.20 -1851390.001591 > 0.30 -1851389.436699 > 0.40 -1851389.760231 > 0.50 -1851389.726310 > 0.60 -1851389.808428 > 0.70 -1851389.907829 > 0.80 -1851389.840644 > 0.90 -1851389.967373 > 1.00 -1851390.061502 > 1.10 -1851390.057500 > 1.20 -1851390.086172 > 1.30 -1851390.042747 > 1.40 -1851390.060210 > 1.50 -1851389.998599 > 1.60 -1851390.120319 > 1.70 -1851390.141846 > 1.80 -1851390.131003 > 1.90 -1851390.170220 > 2.00 -1851390.141617 > 2.10 -1851390.135779 > 2.20 -1851390.255565 > 2.30 -1851390.153947 > 2.40 -1851390.238681 > 2.50 -1851390.144512 > 2.60 -1851390.255200 > 2.633000 -1851390.178012 > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of David van > der Spoel > Sent: Thursday, March 28, 2019 3:10:05 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production > Run > > Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student): >> Hello gromacs users, >> >> >> I am trying to simulate a peptide amphiphile with the CHARMM27 force field. >> To do this I have had to specify an additional bond type and bond, angle, >> dihedral, etc. parameters in the .itp files of the force field. Then, to >> check if I had done this correctly, I minimized the system, and ran a >> production run to generate an NVE ensemble, so that I could make sure the >> system was conserving energy appropriately. After looking at the energy vs >> time plot (produces with the gmx energy command), however, the system jumps >> from an initial energy, up ~20 kJ per mole and then conserves energy for the >> most part (slight drifting but seems tolerable relative to the initial >> discontinuity). Is this discontinuity a normal happenstance or a result of >> bad minimization? >> > Is that at step 0 in the simulation? > > Please check options like > ; Do not constrain the start configuration > continuation = no > > >> >> Thank you! >> >> Luke >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Conservation at the Beginning of a Production Run
In the mdout.mdp file corresponding to this run I have the line ; Do not constrain the start configuration continuation = no Do I need to change this to yes? The plot of energy vs time looks like an under damped response to a set point change in control theory - slight overshooting after the first few steps, then settling down to an average value nicely. This is what is leading me to believe that there is a large, non conservative force near the beginning that becomes smaller, and conservative. Time (ps) 0.00 -1851396.981075 0.10 -1851388.994856 0.20 -1851390.001591 0.30 -1851389.436699 0.40 -1851389.760231 0.50 -1851389.726310 0.60 -1851389.808428 0.70 -1851389.907829 0.80 -1851389.840644 0.90 -1851389.967373 1.00 -1851390.061502 1.10 -1851390.057500 1.20 -1851390.086172 1.30 -1851390.042747 1.40 -1851390.060210 1.50 -1851389.998599 1.60 -1851390.120319 1.70 -1851390.141846 1.80 -1851390.131003 1.90 -1851390.170220 2.00 -1851390.141617 2.10 -1851390.135779 2.20 -1851390.255565 2.30 -1851390.153947 2.40 -1851390.238681 2.50 -1851390.144512 2.60 -1851390.255200 2.633000 -1851390.178012 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: Thursday, March 28, 2019 3:10:05 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production Run Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student): > Hello gromacs users, > > > I am trying to simulate a peptide amphiphile with the CHARMM27 force field. > To do this I have had to specify an additional bond type and bond, angle, > dihedral, etc. parameters in the .itp files of the force field. Then, to > check if I had done this correctly, I minimized the system, and ran a > production run to generate an NVE ensemble, so that I could make sure the > system was conserving energy appropriately. After looking at the energy vs > time plot (produces with the gmx energy command), however, the system jumps > from an initial energy, up ~20 kJ per mole and then conserves energy for the > most part (slight drifting but seems tolerable relative to the initial > discontinuity). Is this discontinuity a normal happenstance or a result of > bad minimization? > Is that at step 0 in the simulation? Please check options like ; Do not constrain the start configuration continuation = no > > Thank you! > > Luke > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy Conservation at the Beginning of a Production Run
Hello gromacs users, I am trying to simulate a peptide amphiphile with the CHARMM27 force field. To do this I have had to specify an additional bond type and bond, angle, dihedral, etc. parameters in the .itp files of the force field. Then, to check if I had done this correctly, I minimized the system, and ran a production run to generate an NVE ensemble, so that I could make sure the system was conserving energy appropriately. After looking at the energy vs time plot (produces with the gmx energy command), however, the system jumps from an initial energy, up ~20 kJ per mole and then conserves energy for the most part (slight drifting but seems tolerable relative to the initial discontinuity). Is this discontinuity a normal happenstance or a result of bad minimization? Thank you! Luke -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy Conservation Conundrum
Hello Everyone, I am a new user to gromacs and I am having trouble with energy conservation in my simulation. After I produced the (solvated and neutralized) configuration and respective topology files I performed an energy minimization that converged to single-precision machine accuracy. After the minimization, I wanted to ensure that the system is conserving energy, so I performed a brief run with no thermo- or barostats in place, constraining only the H-bonds with the LINCS algorithm (lincs-order =4 and lincs-iter =4). I have tried decreasing the timestep from 2 fs to 1 fs and even 0.1 fs to no avail. Any recommendation? Warm regards, Luke -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
