Re: [AMBER] molecules split apart during MD

From: Jason Swails <>
Date: Fri, 10 Jul 2015 10:37:29 -0400

On Fri, 2015-07-10 at 10:20 -0400, Lara rajam wrote:
> Dear Amber !
> I am doing a simulation of a protein complex.
> the protein is having two chains A and B and a ligand.
> I did md for 20 ns in NPT ., when I converted the final md.rst file to pdb
> and viewed it
> the protein chains split apart . what is the mistake I am doing

There is no mistake. What you are observing is a very common imaging
artifact. You can Google "imaging artifact amber" and read all about it
at your leisure.

The take-home message here, though, is that this is not wrong, does not
indicate a problem, and is quite common when using iwrap=1.

If you want a more visually satisfying image (i.e., the representation
where the protein is centered in the periodic box with water surrounding
it), then you can reimage your trajectory with the "autoimage" command
in cpptraj:

cpptraj -p your.prmtop -i input

where input is


Of course, adjust the file names for whatever you have.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 10 2015 - 08:00:02 PDT
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