Re: AMBER: Dummy Atom Types on both states

From: Thomas Steinbrecher <>
Date: Tue, 15 Feb 2005 01:04:06 -0800


> 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 (on
both "sides" of the perturbation) can give rise to the origin singularity
effect, see for example:

T. Simonson, Mol. Physics, 1993, 80:2,441-447

sander is designed to handle such problems by a modified potential mixing
function (setting klambda>1) but that requires to have the dummy atoms
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 work
in progress.

Kind Regards,

Thomas Steinbrecher

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Received on Tue Feb 15 2005 - 09:53:00 PST
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