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

From: Ben Roberts <>
Date: Fri, 30 Mar 2012 13:38:00 +1300

Hi Adam,

On 30/03/2012, at 1:05 PM, Adam Jion wrote:

> 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.

In general, you should be able to set "iwrap = 1" in your input file to force automatic translation of particles back into the box. Furthermore, if you need to do so after the fact, you can use ptraj or cpptraj to create a "wrapped" version of your trajectory.

Hope this helps,

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Received on Thu Mar 29 2012 - 18:00:06 PDT
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