Hi, The virial has no meaning per atom. And you can't get the virial per atom out of Gromacs, it is never calculated in that way (see the manual for details). A special local pressure version of Gromacs exists, but even there you won't get a virial per atom.
Cheers, Berk ---------------------------------------- > Date: Mon, 21 Jan 2013 12:35:04 -0500 > From: [email protected] > To: [email protected] > Subject: [gmx-users] Getting the virial for each individual atom. > > Hello, > For the research I'm working with, I need to get the virial for each > individual atom in the system. I've been tracing all of the calls made in > the methods related to virials(Version 4.5.5) and this is the call stack > that I think has what I need. > mdrun.c -> do_md in md.c -> do_force in sim_util.c -> calcvir.c > > I have a few questions that I was wondering if anyone could answer. > > 1. In sim_util.c, there is a comment that says "Total virial computed in > global_stat, called from do_md". I cannot find where this is called in > do_md. Was this changed at any point and the comment was still left in the > code? > > 2. If I change the codes in calcvir.c to find the virials for each > individual atom, say by piping the atom numbers and forces and everything > needed into another program so it doesn't effect the way that gromacs runs > and will still allow everything to do what it needs, will this be screwed > up by/screw up the domain decomposition/the mpi stuff? > > Basically, I'm looking for advice on a method to output the individual > virials for each atom for each frame, instead of just the final output of > the average virial on the entire system. > Thanks, > Zach Marcin > Wilkes University > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
