[gmx-users] pairlist and nonbonded parameters; a bug?

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 29 22:23:25 CET 2005

David Mobley wrote:
> Dear All,
> As best I can tell from the manual, the [ pairs ] section allows
> manual specification of interaction parameters between pairs of atoms
> and is normally used to modify 1-4 interactions.  However, it seems to
> not be functioning as advertised.
> Particularly, I've been trying to figure out how to turn off only
> intermolecular interactions while leaving intramolecular interactions
> on using the pairlist, as I mentioned previously. I still haven't been
> able to figure out how to do this, but instead, I tried a simple test:
> - Put two LJ spheres in vacuum.
> - Use the pairlist to specify that there are no interactions between
> the two (setting interaction vdW parameters to zero).
> - Perturb the vdW parameters of one of the atoms to zero

Both particles have to be in a single molecule.

> The free energy of doing this should be identically zero if the two LJ
> spheres are noninteracting, as should the potential energy (the
> charges are turned off).
> Instead, I get nonzero potential energies and dv/dlambdas (thus free
> energies) for any calculation which involves perturbing the vdW
> parameters, and even if I don't perturb the vdW parameters, I get
> nonzero potential energies. So clearly the pairlist isn't working to
> set the interaction parameters.
> Can anyone help? Is there something else I need to set? Or is this
> some sort of a bug? Should I attach my topology?

> 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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