[gmx-developers] Monte Carlo Simulations

Fri Feb 3 14:32:45 CET 2012

Hi,

The paper is accepted and we are waiting for the proofs. In the 
meantime, please contact me if you're interested to obtain a copy of the 
manuscript.

Cheers,
René

=====================================================
René Pool

Department of Biological Psychology
Faculty of Psychology and Education
VU University Amsterdam
Van der Boechorststraat 1
1081 BT AMSTERDAM, the Netherlands

Room 2B-05
E: r.pool at vu.nl
T: +31 20 598 38 52
=====================================================

On 02/01/2012 09:38 AM, Anton Feenstra wrote:
> Hi,
>
> 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 SPC water:
> 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.
>>
>> 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: "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
>>>
>>> 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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>>>
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>>
>
>