Hi, I have a system of similar molecules, I would like to obtain the rdf at contact (meaning, at surface of one particle). What I try is; I make an index file containing only central atoms of all molecules, then I run:
gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 -b 14000 ref 0 is a single atom ref 1 is rest of atoms Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg file. My problem is I get very different values for different time intervals (after equilibrium) . Why is that so? I appreciate if sb can help. Best regards -- 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.
