Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
An update to anyone interested: Regenerating velocities by itself did not solve the problem. I had to regenerate velocities and couple the upper and lower leaflets separately to the thermostat to equilibrate the system. To smoothen the equilibration process further, I used a 0.5 fs timestep instead of 2 fs (though this is probably unnecessary). Thank you once more, Tsjerk. Old .mdp: comm-grps= SOL DMPC tcoupl = v-rescale; Thermostat tc-grps = DMPC SOL ; Couple lipids and SOL separately tau-t= 0.1 0.1 ; Time constant for temperature coupling ref-t= 310 310 ; Desired temperature (K) New .mdp: comm-grps= SOL upper lower tcoupl = v-rescale; Thermostat, v-rescale is also fine tc-grps = upper lower SOL ; Couple lipid leaflets and SOL separately tau-t= 0.1 0.1 0.1 ; Time constant for temperature coupling ref-t= 310 310 310 ; Desired temperature (K) On Wed, Nov 13, 2013 at 4:07 PM, rajat desikan wrote: > Hi Tsjerk, > That was very sage advice! Thank you. I will try regenerating velocities > and see if the motion goes away... > > > On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar wrote: > >> Hi Rajat, >> >> If you remove comm on the bilayer, there may be relative comm between >> leaflets. If that relative motion is significant and you switch to >> removing >> comm per leaflet, the program suddenly finds itself resetting the com over >> a large distance. About equilibration, you equilibrated with comm_grps = >> SOL DMPC, the system is not equilibrated for another scheme. You can solve >> this issue by regenerating velocities, or by running short cycles with the >> time step increasing from very small to normal. >> >> Hope it helps, >> >> Tsjerk >> >> >> On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan > >wrote: >> >> > Hi All, >> > Any suggestions? >> > >> > Thanks, >> > >> > >> > On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan > > >wrote: >> > >> > > Hi All, >> > > I am experiencing a few problems in membrane simulations wrt COM >> removal. >> > > I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all >> the >> > > accompanying files. I then carried out the following steps: >> > > 1) energy minimization >> > > 2) NVT Eq - 100 ps >> > > 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) >> > > >> > > Then I used g_select to select the upper and lower DMPC leaflets. The >> > then >> > > carried out a 250 ps NPT eq again. The only change was: >> > > comm-grps= SOL DMPC ==> >> > > comm-grps= SOL upper lower >> > > >> > > On every step in log file, I get the following message: >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > *Step Time Lambda 124000 >> > > 248.00.0 Large VCM(group lower): -0.00051, >> > > -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies >> > > (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 >> > > Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 >> > > -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb >> (SR) >> > > Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 >> -5.84134e+05 >> > > -8.87497e+04 PotentialKinetic En. Total Energy >> Temperature >> > > Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 >> > > 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd >> -1.85927e+02 >> > > 6.42934e-06* >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > *Large VCM(group lower): -0.00187, -0.00369, 0.00032, >> > > Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, >> > > -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): >> > > 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large >> VCM(group >> > > lower): -0.00541, 0.00546, -0.00166, Temp-cm: >> 7.24656e+29 >> > > Large VCM(group lower): -0.00220, 0.00362, -0.00741, >> > Temp-cm: >> > > 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, >> > > 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, >> > > -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): >> > > -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large >> > VCM(group >> > > lower): 0.00252, 0.00594, 0.00068, Temp-cm: >> 4.93342e+29* >> > > *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme >> > > mesh/force 0.636* >> > > >> > > I do not know what to make of it. There are no issues when I remove >> COM >> > > for the entire system. I have seen this issue come up a few times in >> the >> > > archives too, but I didn't find a satisfactory solution since the >> bilayer >> > > was very well eq
Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
Hi Tsjerk, That was very sage advice! Thank you. I will try regenerating velocities and see if the motion goes away... On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar wrote: > Hi Rajat, > > If you remove comm on the bilayer, there may be relative comm between > leaflets. If that relative motion is significant and you switch to removing > comm per leaflet, the program suddenly finds itself resetting the com over > a large distance. About equilibration, you equilibrated with comm_grps = > SOL DMPC, the system is not equilibrated for another scheme. You can solve > this issue by regenerating velocities, or by running short cycles with the > time step increasing from very small to normal. > > Hope it helps, > > Tsjerk > > > On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan >wrote: > > > Hi All, > > Any suggestions? > > > > Thanks, > > > > > > On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan > >wrote: > > > > > Hi All, > > > I am experiencing a few problems in membrane simulations wrt COM > removal. > > > I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all > the > > > accompanying files. I then carried out the following steps: > > > 1) energy minimization > > > 2) NVT Eq - 100 ps > > > 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) > > > > > > Then I used g_select to select the upper and lower DMPC leaflets. The > > then > > > carried out a 250 ps NPT eq again. The only change was: > > > comm-grps= SOL DMPC ==> > > > comm-grps= SOL upper lower > > > > > > On every step in log file, I get the following message: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Step Time Lambda 124000 > > > 248.00.0 Large VCM(group lower): -0.00051, > > > -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies > > > (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 > > > Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 > > > -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb > (SR) > > > Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 > -5.84134e+05 > > > -8.87497e+04 PotentialKinetic En. Total Energy > Temperature > > > Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 > > > 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 > > > 6.42934e-06* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Large VCM(group lower): -0.00187, -0.00369, 0.00032, > > > Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, > > > -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): > > > 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large > VCM(group > > > lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 > > > Large VCM(group lower): -0.00220, 0.00362, -0.00741, > > Temp-cm: > > > 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, > > > 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, > > > -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): > > > -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large > > VCM(group > > > lower): 0.00252, 0.00594, 0.00068, Temp-cm: > 4.93342e+29* > > > *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme > > > mesh/force 0.636* > > > > > > I do not know what to make of it. There are no issues when I remove COM > > > for the entire system. I have seen this issue come up a few times in > the > > > archives too, but I didn't find a satisfactory solution since the > bilayer > > > was very well equilibrated. > > > > > > I would appreciate any suggestions. Thank you. > > > > > > > > > -- > > > Rajat Desikan (Ph.D Scholar) > > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > > Dept. of Chemical Engineering, > > > Indian Institute of Science, Bangalore > > > > > > > > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -
Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM
Hi Rajat, If you remove comm on the bilayer, there may be relative comm between leaflets. If that relative motion is significant and you switch to removing comm per leaflet, the program suddenly finds itself resetting the com over a large distance. About equilibration, you equilibrated with comm_grps = SOL DMPC, the system is not equilibrated for another scheme. You can solve this issue by regenerating velocities, or by running short cycles with the time step increasing from very small to normal. Hope it helps, Tsjerk On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan wrote: > Hi All, > Any suggestions? > > Thanks, > > > On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan >wrote: > > > Hi All, > > I am experiencing a few problems in membrane simulations wrt COM removal. > > I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the > > accompanying files. I then carried out the following steps: > > 1) energy minimization > > 2) NVT Eq - 100 ps > > 3) NPT Eq - 250 ps (Berendsen temp, Pres coupling) > > > > Then I used g_select to select the upper and lower DMPC leaflets. The > then > > carried out a 250 ps NPT eq again. The only change was: > > comm-grps= SOL DMPC ==> > > comm-grps= SOL upper lower > > > > On every step in log file, I get the following message: > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Step Time Lambda 124000 > > 248.00.0 Large VCM(group lower): -0.00051, > > -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies > > (kJ/mol)U-BProper Dih. Improper Dih. LJ-14 > > Coulomb-147.23818e+044.19778e+046.46641e+024.54801e+03 > > -1.45245e+05 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) > > Coul. recip.2.79689e+04 -3.78407e+03 -2.10679e+03 -5.84134e+05 > > -8.87497e+04 PotentialKinetic En. Total EnergyTemperature > > Pres. DC (bar)-6.76497e+051.76468e+05 -5.00029e+05 > > 3.10424e+02 -1.05704e+02 Pressure (bar) Constr. rmsd -1.85927e+02 > > 6.42934e-06* > > > > > > > > > > > > > > > > > > > > *Large VCM(group lower): -0.00187, -0.00369, 0.00032, > > Temp-cm: 2.02076e+29 Large VCM(group lower): -0.00725, > > -0.00278, -0.00549, Temp-cm: 1.05988e+30Large VCM(group lower): > > 0.00020, 0.00308, -0.00176, Temp-cm: 1.48126e+29Large VCM(group > > lower): -0.00541, 0.00546, -0.00166, Temp-cm: 7.24656e+29 > > Large VCM(group lower): -0.00220, 0.00362, -0.00741, > Temp-cm: > > 8.53812e+29Large VCM(group lower): 0.00140, -0.00160, > > 0.00029, Temp-cm: 5.39679e+28Large VCM(group lower): -0.00056, > > -0.00293, -0.00364, Temp-cm: 2.59422e+29 Large VCM(group lower): > > -0.00172, -0.00260, 0.00494, Temp-cm: 3.99945e+29Large > VCM(group > > lower): 0.00252, 0.00594, 0.00068, Temp-cm: 4.93342e+29* > > *DD step 124999 vol min/aver 0.702 load imb.: force 1.3% pme > > mesh/force 0.636* > > > > I do not know what to make of it. There are no issues when I remove COM > > for the entire system. I have seen this issue come up a few times in the > > archives too, but I didn't find a satisfactory solution since the bilayer > > was very well equilibrated. > > > > I would appreciate any suggestions. Thank you. > > > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
