Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this:
DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 1000000 nstxout = 0 nstvout = 0 nstlog = 10000 nstxtcout = 10000 xtc-precision = 10 cutoff-scheme = verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r = 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t = 1.0 1.0 ref-t = 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p = 5 compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim = Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
