Re: [AMBER] Pressure regulation and position restraints

From: David A Case <>
Date: Wed, 9 Mar 2011 11:57:49 -0500

On Mon, Mar 07, 2011, Andrew Jewett wrote:

> For simulations at constant pressure, AMBER presently rescales the
> positions of all atoms, regardless of whether or not they are
> constrained (harmonic or belly restraints). This sometimes results in
> some very strange behaviour. It would be desirable to be able to turn
> this off.
> Unfortunately, changing this is difficult because, presently, the
> forces acting on these atoms are not ignored when calculating the
> virial. If we allow the user to to freeze the immobilised atoms
> (while rescaling the other atoms), then we must modify the way the
> virial is calculated.
> I have attached a document that suggests how to do that, along with
> some code samples.

We are looking into this...thanks...dac

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Received on Wed Mar 09 2011 - 09:00:11 PST
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