[gmx-developers] Monte Carlo Simulations

[André Assunção S. T. Ribeiro]

Hi,

As Michael said, the main problem would be making a consistent framework for several MC move types and compatibility with the MD code. Furthermore, for straight MC simulations, significant changes would need to be made to energy/force evaluation routines and possibly parallelization routines too. I do not know if there would be interest on this. As to the MC moves, as I said earlier, the CRA moves and simple moves for rigid body motion and internal coordinate displacement have been implemented. I am also implementing the CRRUBAR moves of Betancourt (JCP 2005, JCP 2011). There is oubviously a large number of other MC moves for various types of molecules that could be implemented, and if we are able to group of number of people working on this it would be great.

Cheers,
Andre.


________________________________
 De: Jared Thompson <thompson.jared.79 at gmail.com>
Para: André Assunção S. T. Ribeiro <aastr at yahoo.com.br>; Discussion list for GROMACS development <gmx-developers at gromacs.org> 
Enviadas: Quarta-feira, 1 de Fevereiro de 2012 13:41
Assunto: Re: [gmx-developers] Monte Carlo Simulations
 

Andre,
MC/MD is good, but I was thinking more of a robust, state-of-the-art MC simulation platform for GROMACS. I would like to have something like this for my Ph.D. thesis.

~j


2012/1/31 André Assunção S. T. Ribeiro <aastr at yahoo.com.br>  

Hi,
>
>
>Some time ago I sent an email saying that the CRA moves of Ulmschneider and Jorgensen had been implemented in 4.5.3. Since then we have used this code in combination with regular MD and the results seem promising. A paper reporting our earlier results has been recently published (DOI 10.1002/jcc.22925). The code is still based on 4.5.3, but I could put this into the latest development version, if that interests anyone.
>
>
>Cheers,
>Andre.
>
>
>
>________________________________
> De: "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>
>Para: Discussion list for GROMACS development <gmx-developers at gromacs.org> 
>Enviadas: Terça-feira, 31 de Janeiro de 2012 22:31
>Assunto: Re: [gmx-developers] Monte Carlo Simulations
> 
>
>Hi, all-
>
>MC is definitely an interest of mine, and I think I've already volunteered
>to help organize more MC functionality on the core developer side.
>
>Any MC functionality will be part of 5.0 going forward, and will not be in
>any 4.0 version.  The most likely scenario (there's no settled plan yet) is
>to have MC be the parent integrator, and have MD as essentially a
>rejectionless MC variant; this will allow things like hybrid MD/MC, etc.
>The integrator code is too complicated right now, and this will likely be
>part of a larger effort to make the integrators simpler in 5.0.
>
>Right now all
 the developers are concentrating very hard on getting 4.6 out
>the door, so there is not much time to think about it new 5.0 features.  But
>definitely ping me about this as soon as you hear about 4.6 being released,
>and we'll start diving in.
>
>The hard part is not WRITING the MC code, it's fitting it into the rest of
>the code in a smooth way.
>
>Best,
>~~~~~~~~~~~~
>Michael Shirts
>Assistant Professor
>Department of Chemical Engineering
>University of Virginia
>michael.shirts at virginia.edu
>(434)-243-1821
>
>
>> From: Jared Thompson <thompson.jared.79 at gmail.com>
>> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>> Date: Tue, 31 Jan 2012 19:00:32 -0500
>> To: <gmx-developers at gromacs.org>
>> Subject: [gmx-developers] Monte Carlo Simulations
>> 
>> Hi All,
>> 
>> There has been some discussion in the past with regards to developing a
>> Monte Carlo integrator for the gromacs platform. I recently downloaded and
>> poked through 4.5.5 and I can't find anything in it that looks like a MC
>> integrator function (I'm thinking of do_md). Does anyone have an update on
>> that or what? Does anyone feel like helping me develop a nice MC scheme in
>> Gromacs?
>> 
>> ~j
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