Hi, You can follow the advice here for making the visual representation whatever you want. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark On Fri, May 22, 2015 at 10:16 AM Ming Tang <m21.t...@qut.edu.au> wrote: > Dear Mark, > > Thanks a lot. > Is it possible to get the water box fixed through command in .mdp, or > using a specific option to fix the water box, like -nojump for g_traj? > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: Wednesday, 20 May 2015 7:31 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] water box moves during MD simulation > > Hi, > > You can add (say) -1.23 to every x coordinate and you have a description > of the same system. So you can pick any of these for doing the simulation, > and any of these for representing the trajectory afterwards. > > Mark > > On Wed, May 20, 2015 at 11:19 AM Ming Tang <m21.t...@qut.edu.au> wrote: > > > Dear Brother, > > > > What does Mark mean? > > > > Sent from my Huawei Mobile > > > > Mark Abraham <mark.j.abra...@gmail.com> wrote: > > > > 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. > > -- > > 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. > -- > 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.