[gmx-developers] Monte Carlo Simulations

Wed Feb 1 17:34:37 CET 2012

Hi Michael,

I can be mistaken, but, though there are energy-only kernels, I do not remember of an easy way of calculating only a specific set of energy contributions. In MD we always need to calculate everything, but in MC this is not so.

Cheers,
Andre.

________________________________
 De: "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>
Para: André Assunção S. T. Ribeiro <aastr at yahoo.com.br>; Discussion list for GROMACS development <gmx-developers at gromacs.org>; Jared Thompson <thompson.jared.79 at gmail.com> 
Enviadas: Quarta-feira, 1 de Fevereiro de 2012 14:19
Assunto: Re: [gmx-developers] Monte Carlo Simulations

Hi, Andre-

> 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.

There are already inner loops that are energy only, so that's not an issue
-- that level of planning has for MC has been around for a while.  I don't
think the parallelization issues of MC have been thought about as much, but
the current scheme should work fine for a first pass.

> 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.

Once we get the framework in, I think people can definitely go crazy with
the moves.  One other aspect of this is being able to validate move sets
producing the correct ensemble. I have some code working (hopefully paper
sent for review soon) that will be able to do this.

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

> 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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