[gmx-developers] MC with GROMACS

Berk Hess hess at cbr.su.se
Fri Dec 10 12:08:39 CET 2010

We are working on moving to redmine, which would replace bugzilla.
This is not just a bug tracking system, but also a project management
There one can easily make project groups and organize such kind of projects.


On 12/10/2010 12:09 AM, Shirts, Michael (mrs5pt) wrote:
> 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?
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>> 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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