Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi

From: Aron Broom <>
Date: Thu, 29 Mar 2012 20:35:33 -0400

you should open the file up in VMD and make sure this is actually the
case. I'm not sure exactly how the coordinate system works, but if your is
100x100x100 and you are seeing a particle with position 101, 100, 100,
perhaps it is the case that your box is simply no longer centered at
50,50,50. Again, that may be completely rubbish, but I'd open it for
viewing in VMD first just to make sure.


On Thu, Mar 29, 2012 at 8:05 PM, Adam Jion <> wrote:

> Hi!
> I'm simulating a system using pmemd.cuda.mpi.
> However, halfway during the simulation when I looked at the .rstrt file, I
> noticed that some particles are moving outside the simulation box.
> I'm new to Amber, having migrated from Gromacs :-).
> Is this normal? Is there a command to translate the particles back into
> the box.
> Regards,
> Adam
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Thu Mar 29 2012 - 18:00:05 PDT
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