Re: Replica-Exchange MD

From: Paul R Brenner (
Date: Fri Nov 18 2005 - 09:49:38 CST

I'm not familiar with any REM tools internal to NAMD. You can script an REM
simulation external to your MD engine but the output file IO is non-trivial and
there is much more communication overhead. However as the number of REM
temperatures scales with system size an external script works well when
submitting to GRID engines like Condor.

My group maintains the free open source MD/MC software ProtoMol for prototyping
algorithms. ProtoMol is patterned after NAMD but designed with the expressed
intent to more easily design and test new algorithms with minimal impact to the
core simulation objects (Object Oriented C++ design). We have recently added
internal MPI based REM functionality.


Paul R Brenner, P.E.
Computer Science and Engineering
The University of Notre Dame

Quoting Mark Abraham <>:

> >
> > Hi,
> >
> > there were some previous (but apparently unanswered) messages about
> > replica exchange within NAMD, in particular the message by Mark
> > Abraham (maybe there was a reply off-list ??).
> >
> > I would also be very interested in carrying out REMD simulations with
> > NAMD, so I wonder whether any extensions, scripts etc. are available
> > for this ?
> I've heard nothing.
> Mark

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