Berk, Here is where I think I might be able to: In calcvir.c there is a method called calc_vir which takes, among other things, int nxf(no idea what this does), rvec x[], and revec f[]. It then does dvxx+= x[i][xx] *f[i][XX];. This is the same as the formula that I am trying to solve for (Vi*Pi + .5*SUM(Rij * Fij)). What I figured I could do is create another array to calculate the virials for, thus giving me an index position per atom, and then use that somehow.
I also know that I can use R(ij) * F(ij), or the distance between atoms i and j times the Forces between atoms i and j. If anyone has any insight on getting these, that could also work. I know how to get the individual positions, but I don't know how I would go about the forces aspect of that. Thanks, Zach On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess <[email protected]> wrote: > > 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 > -- 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
