[gmx-users] topology file and LJ parameters

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 26 22:36:17 CET 2005

David Mobley wrote:
> Dear all,
> I'm doing a free energy calculation which involves turning off a small
> molecule's interactions with its environment. Ordinarily, for the vdW
> part of this, I simply turn off the vdW interactions of the small
> molecule. However, it would be better to turn off the vdW interactions
> with the environment, ONLY. Someone had mentioned to me it should be
> possible to do this using careful manipulation of the topology file in
> GROMACS, and I've been trying to figure out how to do it, but have
> been unsuccessful.
You mean you want to maintain the intramolecular VdW interactions?
In that case you could specify all the interactions as pairs, with 
parameters different from the normal LJ.
It's only 200...

> Can anyone recommend a way to do this? Here's a couple of ideas I'd
> come up with that I haven't been able to get to work so far (by
> "work", I mean that I've been testing them in a case where I try
> turning off the small  molecule's interactions in vacuum, where
> dv/dlambda for turning off vdW interactions should be zero if I'm
> leaving the intramolecular vdW interactions on; when they don't work,
> the result for this is NOT zero):
> (a) Set up normal and perturbed atom types as usual (where the
> perturbed atom types have vdW turned off) but then specify nonbonded
> interactions for the atom types that I want to have continue to
> interact with one another. For some reason if I do this and have a
> pairlist for 1-4 interactions, I get big contributions to dv/dlambda
> from the 1-4 terms even if I don't actually perturb any of the vdW
> parameters (i.e. if I only change the atom types to equivalent ones).
> (b) Specify in a pairlist all of the pairs I want to have continue
> interacting, with explicit statement of parameters.
> Should it be possible to make this work? If so, can anyone give me 
> some guidance how it ought to work?
> I would also note that my small molecules are quite small (i.e. 20
> atoms) so I'm not opposed to solutions which require explicit
> enumeration of all of the interacting pairs within these small
> molecules.
> Thanks,
> David
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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