AMBER Archive (2002)

Subject: Re: box_size

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Tue Jan 29 2002 - 09:38:55 CST

Its not an option in sander at this point. It wouldn't be all that hard to
alter the code to do it. However I wouldn't venture a guess as to the
outome. The appropriate theory is not implemented in sander. If your
system is big enough (i.e. box size of 40A or more) the size fluctuations
in a stable simulation aren't very big (1/2 angstrom or so). Is there a
reason you need the one dimension defined more precisely than this?
Tom Darden
 On Tue, 29 Jan 2002, Susanna Monti wrote:

> I would like to know if it possible to fix one dimension of the
> simulation box (allowing only changes in the other two dimensions) in a
> PBC NPT molecular dynamics run.
> thanks
> Susanna
>
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