Re: AMBER: Dummy Atom Types on both states

From: <>
Date: Tue, 15 Feb 2005 17:29:39 +0000


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 lambda > 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?


David Evans
School of Pharmacy
University of London
---- Message from Thomas Steinbrecher <> at
2005-02-15 01:04:06 ------
>> Dummy atoms are just atoms (or atom TYPES). They have some
parameters too,
>> except that the non-bonded parameters are set to be zero. Let's
say that I
>The problem with dummy atoms does not lie in sander itself but is a
>statistical effect that makes your results unreliable. Dummy atoms
>both "sides" of the perturbation) can give rise to the origin
>effect, see for example:
>T. Simonson, Mol. Physics, 1993, 80:2,441-447
>sander is designed to handle such problems by a modified potential
>function (setting klambda>1) but that requires to have the dummy
>only in one state, because the modification that prevents the origin
>singularity for dummies in the perturbed state would make it even
>bigger for dummies in the ground state.
>I have tried a code-modification to prevent this, but it is still
>in progress.
>Kind Regards,
>Thomas Steinbrecher
>The AMBER Mail Reflector
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Received on Tue Feb 15 2005 - 17:53:00 PST
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