[gmx-users] RDF between larger molecules

[Justin Lemkul]

On 1/20/20 9:48 AM, Gmx QA wrote:
> 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?

Yes, likely. You could in principle have a COM-COM RDF value very close 
to r=0 if a lipid were to wrap around a drug molecule, so I don't think 
any of your results are unexpected.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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