From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Mar 21 2007 - 09:54:38 CDT
Hi Alessio,
you can use NBFIX terms in your parameter file for this:
NBFIX
type1 type2 epsAB sigmaAB
Peter
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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