[gmx-users] RDF between larger molecules

[Gmx QA]

Hi list,

I am working on a system that contains lipids, but since there is no water
present they do not form a typical bilayer.

In these systems I also have some smaller drug-like molecules. What would
be the best way to get a proper rdf-function between the lipids and the
drugs? Since both types of molecules are larger than single atoms, I tried
to calculate a com-com rdf using

-selrpos whole_mol_com -seltype whole_mol_com

but the resulting curve is very rugged (i.e. not as smooth as
the atom-rdf's typically shown). The minimum distance (the distance
below which the pdf is zero) also appears to be quite small, since one the
molecules is a lipid I would have expected a larger distance than
the corresponding value seen in e.g. an oxygen-oxygen rdf for water.

Might all of this be consequences of the fact that I have a com-com rdf
between a limited number of molecules?

Thanks
/PK