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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.