Hello I am trying to analyze the interactions between an OH group of 8 (identical) drug molecules with water
1) I do an Hbonds analysis by running g_hbond with an index file containing the OH of all drug molecules as the first group and all water molecules as a second group. The average Hbonds from the hbnum.xvg plot is ~4.8. If divide this by 8 (the number of molecules), we get 0.6/molecule 2) I calculate the RDF using exactly the same two groups (OH of all drug molecules and water). But the integration of the RDF yields 0. I run g_rdf with the default -rdf option (atom). How is this disagreement can be explained? Thanks Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
