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

From: Ross Walker <>
Date: Fri, 30 Mar 2012 10:34:17 -0700

Hi Adam,

> I used the 'iwrap = 1' function in my input file but still got
> particles moving out of the box when I looked at the .rsrt file.
> My simulation box is a triclinic cell.
> Is this an inevitable feature of pmemd.cuda.mpi?
> Can I get the particles to stay within the simulation box without post-
> simulation modifications?
> Or is there something wrong with the implemenation in my input file
> (see below).

We will need to see your input files in order to investigate this further.
In particular specifically what you mean by particles not staying within the
simulation box. Both PMEMD and Sander by default track the coordinates of
the original molecule, I.e. as it moves out of the central box it is imaged
internally (in that fractional coordinates are used) but the coordinates
that get tracked are that of the original molecule. Trajectory files can be
reimaged later in ptraj to recenter things etc. Setting iwrap will cause the
trajectory file coordinates to be imaged as a 'molecule' moves out of the
central box. The key here is molecule, AMBER only images based on molecules,
not atoms, so you can get individual hydrogen's in water appearing to poke
out of the edge of a box. You can also get whole chunks of your protein
appearing to stick out of the box. This is purely a visual artifact though
and can be 'fixed' by post processing with ptraj.

That said there could be an issue with the way your box is defined that is
leading to problems but we'll need a lot more information to be able to
track that down. One thing you should consider trying if you believe this is
a bug with the CUDA code is to run with the cpu version of pmemd (or sander)
and see if the behavior is different.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Fri Mar 30 2012 - 11:00:04 PDT
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