[gmx-developers] MC with GROMACS

[Haiqing Zhao]

Hi,
Actually I'm also paying attention on gmx-mc. However, in my work, some simple version on which only move in dihedral space(i.e fix bond length and bond angles) is OK.
Anyway, I agree to set up a separate discussion group since a breakthrough will come.

cheers
Haiqing



----- Original Message -----
From: "René Pool" <r.pool at vu.nl>
To: "Discussion list for GROMACS development" <gmx-developers at gromacs.org>
Sent: Friday, December 10, 2010 4:54:27 AM GMT -05:00 US/Canada Eastern
Subject: Re: [gmx-developers] MC with GROMACS

Nice work André!
What version of gromacs are you working with? (if I remmeber correctly, 
it was 3.something).
I'd be happy to make the GCMC module compatible with that version as 
well as make it compatible for the latest version of gmx. Keep in mind 
that for now it only works for the LJ system, but it's the first step 
towards GCMC with 'real' molecules.

I agree with Michael that it would be a good idea to have a separate 
discussion group for more specialized stuff. I have no idea how many 
people are interested in gmx-mc? If the interest is too low, a separate 
discussion group could be overkill.

Cheers,
René

=====================================================
René Pool
IBIVU/Bioinformatics
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands
Room P120
E: r.pool at few.vu.nl
T: +31 20 59 83714
F: +31 20 59 87653
=====================================================


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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