[gmx-developers] MC with GROMACS

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Fri Dec 10 00:09:23 CET 2010

So, this reminds me about having separate focused discussion groups on
important general topics for future and current development in Gromacs like
Monte Carlo and free energy calculations.  How are any plans for this going
right now?  It would be a shame if potentially good contributions like this
ended up not being incorporated because they were written in a way that made
it hard to integrate in, or if multiple people are working independently on
the same functionality in an incompatible way.

I'm willing to moderate a free energy calculation group.  It can be as
simple as a separate gmx-XXXXX at gromacs.org mailing address, and wouldn't
necessarily need to be publically indexed.    How difficult would this be to
set up?

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

> From: "André Assunção S. T. Ribeiro" <aastr at yahoo.com.br>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 9 Dec 2010 17:59:50 -0500
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] MC with GROMACS
> Dear all,
> I have implemented the concerted rotations approach of Ulmschneider &
> Jorgensen (JCP,2003) for MC moves of peptides. That has been shown to be very
> efficient coupled with GBSA solvation. This adds to already implemented
> routines for simple MC moves, such as bond stretching and angle bending.
> I have tested the algorithm for detailed balance and also performed
> simulations of alanine polypeptides with GBSA solvation, starting from fully
> extended configurations. The results obtained with MD and MC are equivalent.
> cheers,
> Andre.

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