Re: Dummy atoms in free energy calculation

From: David A. Case <>
Date: Sun 12 Jan 2003 23:37:35 -0800

On Sat, Jan 11, 2003, Lepsa wrote:

> I'd like to ask about what rules there are for choosing the parameters for
> dummy atoms. Specifically, I have an H1 atom and a dummy "attached" to it.
> This will be "mutated" into OH - HO. For the dummy, should I use both the
> bond parameters as in OH-HO or just the equilibrium value or totally
> different? What then? What about other parameters?
> Or could yopu point me to some literature where this problem is dealt with?

I think the simplest thing is to use the bond lengths and force constants
as in OH-HO, and to use thermodynamic integration. If you don't want to do
this (and it may or may not be the most efficient way), you need to think
about the potential of mean force (PMF) for changing the bond length. A
good introduction to all these issues is in:

%A D.A. Pearlman
%A B.G. Rao
%T Free energy calculations: Methods and applications
%P 1036-1061
%B Encyclopedia of Computational Chemistry
%E P. von R. Schleyer
%E N.L. Allinger
%E T. Clark
%E J. Gasteiger
%E P.A. Kollman
%E H.F. Schaefer, III
%I John Wiley
%C Chichester
%D 1998

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Sun Jan 12 2003 - 23:37:35 PST
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