>I would have chosen the groups in the opposite manner. You're interested in the >presence of water around the chosen arginine residue, not the presence of >arginine around water, right? Given this order of chosen groups, the RDF seems >to make sense (very low probability that arginine is close to all water >molecules), though it doesn't represent what you likely want.
>-Justin Of coarse, I'm interested in the presence of water around the arginine. But I did reverse order of groups, i.e. I toke water as the "1 group" and arginine sige chain tip as the "reference group", however have obtained absolutely the same curve. May be there exist some peculiarity in using g_rdf dialog to select groups? -Igor -- View this message in context: http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001p5003088.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
