Dear GMX Users, Sorry to take your valuable time. I have a mixed liquid system simulated using gromacs version 5.0.4, where I want to calculate radial distribution between molecule type A and type B defining the distance between them by either "center of mass of Molecule A" - " closet atom to Molecule A in molecule B" or " closet atom to Molecule B in molecule A" - " closet atom to Molecule A in molecule B" . Looks like it can be solved using gmx rdf option " -surf", however I found in an earlier post that by Dr. Berk Hess saying "g_rdf -surf mol counts the number of atoms within a distance r from the surface,"
We tried something like gmx rdf -f AB.xtc -s AB.tpr -o AB.xvg -surf mol -rdf mol_com << EOF 2 3 EOF # 2 - molecules A, 3- molecules B it gives an unnormalized curve as said in the manual. My question is, will this command give what I want after normalization? If not, is there any other option in gmx that can do what I want? What else package would you suggest to use if this function is not available in gmx? Thank you in advance, Boning Wu Graduate Student, Rutgers University -- 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.
