Hello everyone, I have run simulation of protein interacting with the infinite slab of polymer surface and now I'm trying to calculate the distance between protein geometrical center and the closest atom of the surface. I have read through the manual but still don't understand how to measure such distance with gmx tools. I have come up with the command below:
gmx distance -f protein-surface.trr -s protein-surface.tpr -n protein-surface.ndx -oav protein-surface_dist_oav.xvg -select 'cog of group "Protein" plus cog of group "Surface"' However, as far as I understand it calculates distance between geometric centers of protein and polymer slab, which is not what I am looking for. Is there a way to select "surface" NOT "cog" for the distance measurement between groups? Thanks in advance! Wei-Ta Li -- 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.