[gmx-users] water box moves during MD simulation

[Mark Abraham]

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.tang at 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-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Wednesday, 20 May 2015 7:31 PM
> To: gmx-users at 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.tang at qut.edu.au> wrote:
>
> > Dear Brother，
> >
> > What does Mark mean？
> >
> > Sent from my Huawei Mobile
> >
> > Mark Abraham <mark.j.abraham at 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.tang at 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.
> > > --
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