[gmx-users] topology file and LJ parameters

David Mobley dmobley at gmail.com
Sat Nov 26 22:31:22 CET 2005

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.

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


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