Re: AMBER: Dummy Atom Types on both states

From: David A. Case <>
Date: Tue, 15 Feb 2005 14:26:21 -0800

On Tue, Feb 15, 2005, wrote:
> Just a question to clarify this for myself:
> Is this asymmetry because the equation (5) on page 133 of the Amber8
> manual is asymmetric about
> lambda = 0.5 when klambda > 1?


> Gromacs, and probably other codes, use a 'soft core' potential, which
> is apparently symmetric. So this could perhaps allow simulations with
> dummy atoms at both end-points. But I haven't done any proper
> experimenting. Is this related to what you (Thomas) are doing?

I don't know of any efforts to put soft-cores into Amber. Thomas is working
on an extension to the Eq. (5) mentioned above to remove the restriction
that dummy atoms cannot be placed at lambda=0. (Thomas: I will reply to
your last writeup sometime [soon]!)

(Note that I am not yet convinced that soft cores are really necessary: but
I could be converted!)


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Received on Tue Feb 15 2005 - 22:53:01 PST
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