Res: [gmx-developers] MC with GROMACS

[André Assunção S. T. Ribeiro]

Hi René,


The latest coding was done with version 4.5.3. I have not merged my git 
repository with GROMACS for quite a while (the last time I tried somethings did 
not work). I will send a link with the updated and merged git repository as soon 
as possible, probably by monday.

I will try to keep the code as clean as possible (with few modifications to MD 
code), which also means it wont be as fast as it could. I would love if someone 
could take a look at the code and see if it could be easily integrated with the 
official version.

I totally agree with the specialized discussion groups.

cheers,
Andre.





________________________________
De: René Pool <r.pool at vu.nl>
Para: Discussion list for GROMACS development <gmx-developers at gromacs.org>
Enviadas: Sexta-feira, 10 de Dezembro de 2010 7:54:27
Assunto: 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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