Res: [gmx-developers] MC with GROMACS

[René Pool]

Hi André

Ah, that means I need to make the GCMC module compatible with the latest 
gmx version in the near future. As far as integrating your code with the 
official version, I don't think I'm the right person to say something 
about that...

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
=====================================================


André Assunção S. T. Ribeiro wrote:
> 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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