On Wed, Mar 05, 2003, amber.heimdal.compchem.ucsf.edu wrote:
>
> when i switch to npt md then there is a raise in density at a certain point
> followed by a drop and the simulation stops for ewald bomb reasons.
Do you know what the density should be? Is it ever close to being correct?
> obviously there is some vlimit exception.
Are you saying this because there are "vlimit" error messages? Or is it
obvious to you for some other reason? Can you look at what these system
is doing when the first vlimit messages occur?
Suggestions: 7 Ang. is a pretty short cutoff; try 9 to be safer. Run some
shorter simulations, stop right before bad things happen (density drops)
and see if anything looks funny.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.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
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Received on Mon Mar 10 2003 - 06:53:01 PST
