[gmx-users] How to find the loading capacity of a nanostructure?

[faride badalkhani]

Dear all,

I have performed 50 ns of production MD simulation on a polymer that
contains several drug molecules. Now I need to find how many drugs (and
which ones) remain encapsulated into the polymer. I measured the COM
separation distance between polymer and each drug. However, the problem is
that the results obtained from MD trajectories to calculate the number of
complexed drugs are not in line with the COM distance plots.

Is that correct to consider drugs as part of a supramolecular complex if
they remain at distances shorter than or equal to Rg of the polymer
measured from the center of mass of the polymer along the simulation run.

I have used the following command
 gmx cluster -s md.tpr -f md_nopbc.xtc -n index.ndx -dist com_rmsd-dist.xvg
-o com_rmsd-clust.xpm -cutoff 1.4 -tu ns
but I do not know if it is correct.
I have chosen 1.4 nm as cutoff because the radius of gyration of polymer is
about 1.4 nm.

any help will be greatly appreciated.

Regards,
Farideh