Hi, 100 ns is overkill for those liquids. It should be smooth enough at 1 ns, provided you average g(r) over every molecule. What do you mean the volume decreases? With time?
As for the cut-off, it's well known that switching Coulomb terms leads to artifacts, and increasing the cut-off distance doesn't necessarily make things converge. See http://pubs.acs.org/doi/abs/10.1021/ct0502256 for example. Use PME for electrostatics. Regards, -- Will --- On Sat, 1/30/10, nishap.pa...@utoronto.ca <nishap.pa...@utoronto.ca> wrote: > From: nishap.pa...@utoronto.ca <nishap.pa...@utoronto.ca> > Subject: [gmx-users] rdf > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Saturday, January 30, 2010, 9:45 PM > Hi, > > I am doing rdf's of simple molecules. I ran my > simulation of water and methane for 100ns to get a smoother > curve for the rdf. I am trying to determine the volume, and > after a certain cut-off I would assume my values to be > constant (i.e. volume), but the values fluctuate alot (i.e. > decreasing). If I am using 'switch', from say 0.8-0.9, > shouldn't the values smooth off after 0.9nm? and stay > constant after that? Any insights would be helpful. > > Thanks. > > Nisha P > > > --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/search before posting! > Please don't post (un)subscribe requests to the list. Use > thewww interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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/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/mailing_lists/users.php
