[gmx-developers] Monte Carlo Simulations
feenstra at few.vu.nl
Wed Feb 1 09:38:30 CET 2012
Just plugging in our work, since I believe it will be relevant ;-)
(and my apologies if it turns out not so)
A post-doc in our group, René Pool, has implemented a grand-canonical
Monte Carlo scheme using the GromPy gromacs-python interface. It is
based on library calls to the gromacs md engine from python, and
therefore can be very flexible. In our tests, it is just about as
efficient as a fully gromacs-internal implementation could be (i.e., the
overhead due to python etc, it only a few percent).
There is an open source repo for GromPy
at gitub: https://github.com/GromPy
There's a paper coming out in JCC soon, describing the interface and its
performance in calculating the critical properties of a LJ system and of
Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of
GROMACS Through the GromPy Python Interface Module
René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C.
Smith, and K. Anton Feenstra
René, is the paper far enough along that we can send people the manuscript?
You may search this list for other posts on this work.
On 01/02/12 02:53, Shirts, Michael (mrs5pt) wrote:
> Hi, Andre-
> Having an implementation of the CRA moves would be great, since those are
> complicated. Again, the MAIN problem is putting together a general MC
> framework for all the different move types -- putting the code into the
> current framework probably won't be that useful. I'll be keeping track of
> the interested names; once 4.6 is out the door, we can start talking about
> the best way to put everything together in 5.0.
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
>> From: "André Assunção S. T. Ribeiro"<aastr at yahoo.com.br>
>> Reply-To: "André Assunção S. T. Ribeiro"<aastr at yahoo.com.br>
>> Date: Tue, 31 Jan 2012 17:30:13 -0800
>> To: "michael.shirts at virginia.edu"<michael.shirts at virginia.edu>, Discussion
>> list for GROMACS development<gmx-developers at gromacs.org>
>> Subject: Re: [gmx-developers] Monte Carlo Simulations
>> 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.
>> 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.
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>>> 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
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-developers-request at gromacs.org.
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
|( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
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| | Just Like Any Other Country it Will Break You" (Gogol |
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