I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5 nm.----- Message from "Pandya, Akash" <akash.pandya...@ucl.ac.uk> --------- Date: Mon, 31 Jul 2017 07:29:19 +0000 From: "Pandya, Akash" <akash.pandya...@ucl.ac.uk> Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] RDF Values To: gmx-us...@gromacs.org
Hi all, I am calculating the RDF from a particular residue to a particular glycine molecule. I created an index file for both to do this. My simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my trajectory and all the components stay inside the box. Please could someone tell me how to overcome this issue? My command line is below: gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 60000 -ref -sel -bin 0.5 -norm rdf Akash -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
----- End message from "Pandya, Akash" <akash.pandya...@ucl.ac.uk> ----- -- 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.
