Re: [AMBER-Developers] Possible bug with ntt=3 and ntr=1 - Possible Fix for PMEMD.

From: case <>
Date: Tue, 7 Jul 2009 23:41:38 +0100

On Tue, Jul 07, 2009, Ross Walker wrote:
> So it looks like nscm is getting set to 1000 both in sander and pmemd
> regardless of the value of ntr.

> This seems to run the nucleosome run nice and stable with the behavior I
> expect. Anyone got any comments?

Why is repositioning necessary at all if you have restraints? Plus, your idea
doesn't seem to take into account restarts -- if you've been changing the
reference coordinates on the fly, you'd have to write them out somewhere in
order to be able to restart. But "reference coords are just that: a reference
that should not change.

My vote is to just enforce nscm=0 when ntr=1. However, I can't reproduce your
report using sander: if I set ntr=1 in a gb calculation, nscm is printed out
as 9999999, not 1000. So, you might want to do some quick debugging here.


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Received on Tue Jul 07 2009 - 18:09:40 PDT
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