[gmx-users] water box moves during MD simulation

[Ming Tang]

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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