Re: AMBER: problems with periodic boundary conditions

From: David A. Case <>
Date: Fri, 5 Sep 2003 07:43:29 -0700

On Fri, Sep 05, 2003, Monika Fuxreiter wrote:
> To run MD we are using sander in amber 7. What happens in the run,
> that waters at the boundary start to move away and the density
> condsiderably decreases near the edges. This does not seem to be a boxing
> problem, that few waters are translated to other cells. It appears as a
> problem with periodicity.

Have you used the image command in ptraj to re-translate all the waters back
to the same unit cell? You say that it does "not seem to be a boxing
problem", but I don't know why you think this. If the energy and temperature
are stable, there is probably not a problem. Have you done a constant
pressure equilibration to get the correct overall density? If your overall
density is too low, that might also lead to what you describe.

As far as I know, sander7 should have no problems with prmtop files created
from Amber, version 5.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Fri Sep 05 2003 - 15:53:01 PDT
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