Re: user defined L-J parameters

From: Arturas Ziemys (
Date: Wed Mar 21 2007 - 08:59:21 CDT


I would ask about the same in different way.

If I have particle with OPLS in TIP3. How the interaction should be calculated: with or without vdwGeometricSigma?


>-----Original Message-----
>From: Neelanjana Sengupta []
>Sent: Wednesday, March 21, 2007 12:05 PM
>Subject: Re: namd-l: user defined L-J parameters
>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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