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 -- 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. 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