Dear Gmx Users, I run long simulation of my protein with 50 small molecules in water. I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com. Please, take a look at my plot:
http://speedy.sh/tmJbD/rdf-P-W.png Could you please, explain me why the second peak is so high? Shall I use option -nopbc ? How can I obtain the density [kg/m3] versus the distance? I wish to compare it with RDF of Protein-Ligands so wish to use some normalization for them to be comparable - peaks will be visible. Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
