Re: AMBER: Dummy Atom Types on both states

From: <>
Date: Tue, 15 Feb 2005 18:13:57 +0000

I meant
asymmetric about lambda = 0.5 when kappa > 1

David Evans
School of Pharmacy
University of London
---- Message from at 2005-02-15 17:29:39
>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 - 18:53:00 PST
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