[gmx-users] topology file and LJ parameters
dmobley at gmail.com
Sat Nov 26 23:38:28 CET 2005
> 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...
Yes, that's exactly what I want to do. A couple questions on how that
works in practice:
(a) What do you mean by "with parameters different from the normal LJ"?
(b) Right now I'm trying a test case for which the answer should be
zero (perturbing the vdW parameters for one atom of a larger molecule
in gas, while trying to leave the intramolecular terms on. I'm getting
a nonzero (around 0.5kJ/mol) value for dvd/lambda. Here's exactly what
- Defined a dummy atom type in the topology file (atom types section)
with vdw sigma and epsilon of zero
- Perturbed the atom type in question to this dummy atom type in the
- Enumerated all of the non-excluded (nrexcl=3) interactions involving
this atom type in the pair list and set the vdW parameters to
correspond to what their unperturbed value should have been. (As I
understand it, actually, the value here shouldn't matter; that is, it
shouldn't be perturbed by perturbing the atom type so it should make
no contribution to dv/dlambda. Is that correct?).
Any idea why this wouldn't be working (that is, why it would be giving
me nonzero dv/dlambda values)?
> > 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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