Re: dummy atoms and FEP

From: Christophe Chipot (
Date: Thu Apr 06 2006 - 12:19:06 CDT


our experience has been that using a real sodium ion which is annihilated
concomitantly as a titrable amino acid is mutated into a neutral one is
probably your safest bet. This issue is discussed in detail by:

(1) Donnini, S. et al. J. Comput. Chem. 2005, 26, 115-122.

(2) Henin, J. et al. Biophys. J. 2006, 90, 1232-1240.


> Im still fighting with the FEP....but new quiestions arise all the
> I need to make a Na ion dissapear from my system to keep it neutral
(for PME)
> but I dont know if I should put just a DUM atom (using the charmm 22
> parameters and topologies) with 0 charge 0 mass or a Na ion without
> (dont know well how to do this). The reason for my question is that I
> need the charge to dissapear in my FEP, ant the DUM atom has tha
radii of the
> H atom I think....
> Is that simple, replace the Na for a DUM or it requires some other trick?
> please Help


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


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