Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC.
The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Your suggestions would be appreciated. Thanks in advance. Sincerely, Shima -- 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
