[gmx-users] Radial distribution function

[Sohaib. Mohammed]

Dear all,

I have done a simulation for asphaltene in an organic solvent. The
simulation produces a one cluster contains all the asphaltenes molecules in
the system. I want to calculate the RDF and the cluster profile (i.e.
maximum cluster, average cluster, etc.). Both of them shows strange
results. For example, I simulated N asphaltene molecules, but RDF and
cluster size show both g(r) and MAX Cluster >> N even when I specify the
calculation wrt center of mass of the molecule. The commands I used for the
RDF and max. clust., respectively, as follows:

gmx rdf -f a.xtc -s a.tpr -n index.ndx -o rdf.xvg -selrpos mol_com
gmx clustsize to calculate cluster size

As I think, the maximum cluster should less than or equal to N.

Appreciate any suggestions/comments.

Thank you,
Sohaib