On Sun, Dec 21, 2003, Ran Ye wrote:
>
> I'm basically following the steps on the "DNA"
> tutorial
> to do some MD on proteins. I couldn't get my dynamics
> going because "vlimit exceeded" and "Coordinate
> resetting (SHAKE) cannot be accomplished". Does anyone
> know how to fix it?
In addition to what Bill Ross suggested, don't try a constant pressure
simulation until you have reached a good temperature at constant volume,
turn down the size of the restraints (from 500 to about 5), and use a
larger value of taup (say 2-5) when you _do_ use constant pressure.
...hope this helps...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 Wed Jan 14 2004 - 15:53:11 PST