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 <rajatdesi...@gmail.com>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 <tsje...@gmail.com>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 <rajatdesi...@gmail.com >> >wrote: >> >> > Hi All, >> > Any suggestions? >> > >> > Thanks, >> > >> > >> > On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan <rajatdesi...@gmail.com >> > >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 >> > > 248.00000 0.00000 Large VCM(group lower): -0.00051, >> > > -0.00515, -0.00652, Temp-cm: 8.11828e+29 Energies >> > > (kJ/mol) U-B Proper Dih. Improper Dih. LJ-14 >> > > Coulomb-14 7.23818e+04 4.19778e+04 6.46641e+02 4.54801e+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 Potential Kinetic En. Total Energy >> Temperature >> > > Pres. DC (bar) -6.76497e+05 1.76468e+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 list gmx-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 list gmx-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 >> > > > > -- > 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 list gmx-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