[gmx-developers] modifying replica exchange to allow Hamiltonian exchanges

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sat Feb 26 03:46:44 CET 2011

This has been added in a branch, and the plan is for this functionality to
be included in the next Gromacs release.  We can discuss whether it would be
useful for specific individual to use this test code right now, or whether
it may be best to wait until there has been a chance for it to be tested
more.  There area a number of other free energy changes included in this
code as well.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Ilja Khavrutskii <ivkhavru at gmail.com>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Fri, 25 Feb 2011 18:39:28 -0500
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] modifying replica exchange to allow Hamiltonian
> exchanges
> Hi,
> I would like to add a simple functionality for FEP/TI calculations
> within GROMACS that would use replica exchange routines to do
> exchanges between different lambda values. I have this implemented at
> present via an external perl script, but that is not very efficient
> due to I/O considerations and the need to restart the simulations
> following the exchanges.
> Can someone point out if this capability already exists and if not
> what would be the best place to start digging into the relevant code
> portions?
> Thank you,
> -Ilja
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