[gmx-users] water box moves during MD simulation

[Mark Abraham]

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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