Re: user defined L-J parameters

From: Neelanjana Sengupta (
Date: Wed Mar 21 2007 - 07:05:52 CDT


Good question! Additionally, is it possible to specify that only
certain interactions
be calculated using the vdwGeometricSigma (with all others being calculated
with the Bertholodt rules)?


On 3/21/07, Alessio Alexiadis <> wrote:
> Hi everybody,
> If we have atoms A and B in a certain configuration and we provide in the
> parameter files the LJ parameters sigmaA, sigmaB, epsilonA and epsilonB,
> NAMD uses the Berhtelet-Lorenz rules to combine these parameters and
> calculate sigmaA-B and epsilonA-B. If you specify:
> vdwGeometricSigma yes
> it uses the geometric mean also for sigma. All this seems pretty
> straightforward. The question now is: is it possible to use some other
> user-specified values for sigmaA-B and epsilonA-B, which do not come from
> the geometric or arithmetic mean? Do somebody know if and how this is
> possible?
> Thanks
> Alessio
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Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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