[gmx-users] RDF between larger molecules

[Gmx QA]

Thanks Justin!

Can you also comment on the other issue, the lack of smoothness? I guess
this is because I don't have that many individual coms per bin to
accurately compute the rdf? At least I think that makes sense since when I
increase the value of -bin in gmx rdf I get an increase in "smoothness" and
fewer "jump" back and forth.



Den mån 20 jan. 2020 kl 15:50 skrev Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
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