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 0.00000Large 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+29Large 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+29Large 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+29Large 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 -- 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
