Hi, Nothing wrong with the .mdp file. But you should check your assumption that there's a single meaningful location where an infinite periodic system should be located :-) There's lots of equivalent representations, so mdrun suits itself.
Mark On Wed, May 20, 2015 at 9:05 AM Ming Tang <m21.t...@qut.edu.au> wrote: > Dear all, > > After MD dynamic simulation for 100 ps, I found the water box was moving > during the simulation, but my protein was inside the water box all the time. > Here is the . mdp file I used: > > integrator = md > dt = 0.001 > nsteps = 100000 > nstxout = 1000 > nstvout = 1000 > nstlog = 1000 > nstxout-compressed = 100 > xtc-precision = 10 > cutoff-scheme =verlet > rlist = 1.4 > coulombtype = reaction-field-zero > coulomb-modifier = potential-shift-verlet > rcoulomb-switch = 0.8 > rcoulomb = 1.4 > epsilon_r = 15 > vdw-modifier = potential-switch > rvdw-switch = 0.8 > rvdw = 1.4 > tcoupl = v-rescale > tc-grps = Protein non-protein > tau-t = 1.0 1.0 > ref-t = 300 300 > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau-p = 12.0 > compressibility = 3e-4 > ref-p = 1.0 > refcoord_scaling = all > pbc = xyz > constraints = h-bonds > > Could anybody tell me what's wrong with my .mdp file? > > Thanks in advance. > -- > 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. > -- 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.