AMBER Archive (2003)

Subject: Re: AMBER: problems with periodic boundary conditions

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 05 2003 - 09:43:29 CDT


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: case_at_scripps.edu 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 | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu