[gmx-users] water box moves during MD simulation

[Ming Tang]

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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