On Thu, Apr 7, 2011 at 6:35 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Apr 06, 2011, git repository hosting wrote:
> >
> > commit e6a48cd21926796aea3947f970b914530cad1b21
> > Author: Jason Swails <jason.swails.gmail.com>
> > Date: Wed Apr 6 17:44:38 2011 -0700
> >
> > Add a multi-sander like feature to pmemd (multipmemd)...
> > Currently only T-REMD is implemented,
> > but H-REMD and multi-D-REMD are upcoming.
>
> This sounds great! But I'm hoping that all these variants of REMD are in a
> single place, with an eye towards a "general" REMD capability, that would
> allow the user (perhaps only by modifying the code) to specify which
> exchanges
> should be tried, and what criterion should be used for acceptance. We want
> to
> facilitate exploration of new ideas, and not just hard-wire a series of
> "xxx-REMD" options.
>
The multi-D-REMD should be this generalized functionality. For a
generalized, N-dimensional replica exchange simulation, I can't see how more
exchanges than just basic T-REMD (where only T exchanges because the rest of
the hamiltonian is the same) and H-REMD (where the coordinates exchange and
recalculate energies, so we have 4 energies total) could be needed to make
it as general as possible (and then just allow for an arbitrary number of
exchanging dimensions). I could imagine that people would want to change
the acceptance criteria, but that's all centrally located in remd.fpp, so it
shouldn't be too hard.
My current plan is to parse an input file that maps all of the exchanges
that are supposed to take place; an input file that could easily be
script-generated or hand-generated for those that wish to fine-tune their
REMD experience :)
All the best,
Jason
> ...dac
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 07 2011 - 08:30:07 PDT
