[gmx-developers] MC with GROMACS

[Shirts, Michael (mrs5pt)]

Hi, Berk-

That sounds great!  What is the timeline, do you think?

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Berk Hess <hess at cbr.su.se>
> Date: Fri, 10 Dec 2010 06:08:39 -0500
> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>, Discussion
> list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] MC with GROMACS
> 
> We are working on moving to redmine, which would replace bugzilla.
> This is not just a bug tracking system, but also a project management
> system.
> There one can easily make project groups and organize such kind of projects.
> 
> Berk
> 
> 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.
>>>     
>>   
>