Second what Jason said. It's been awhile since I messed with that code,
but I may get back to it soon. (Get back to the concept and implementation
of our Monte-Carlo barostat--I'm planning to phase out the dynamics
routines in mdgx.)
On Tue, Mar 21, 2017 at 5:41 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Mar 21, 2017, at 4:52 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> >
> > Hi
> >
> > In the barostats.F90 code, both in sander and pmemd, there is term that
> > uses the number of molecules in the box as part of the MC delta H.
> >
> > Can anyone explain why we are using the # of molecules and not the # of
> > atoms ?
>
> Because scaling is done by molecule, not atoms. That is, molecules are
> translated rigidly.
>
> Mdgx does atomic scaling, but there's more complexity there in satisfying
> constraints.
>
> All the best,
> Jason
>
> >
> > Thanks
> >
> >
> >
> > --
> > Dr. Adrian E. Roitberg
> > University of Florida Research Foundation Professor.
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Mar 21 2017 - 22:30:03 PDT
