AMBER Archive (2005)

Subject: Re: AMBER: SHAKE error

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 25 2005 - 18:57:02 CDT

On Sat, Jul 23, 2005, Agata Jurkiewicz wrote:

> But maybe the initial geometry od dUMP is a problem which I can't see
> at once, examining the pdb file? Should I run vacuum calculation with
> dielc=4 to test the initial geometry?

I think that running a vacuum simulation with dielc=4 is a good idea. It will
go very fast, and will help isolate the problem: if you still get failures
here, it is probably a force-field related problem that has little or nothing
to do with water, periodic boundary conditions, how fast you heat up, etc.

...regards...dave

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