[gmx-developers] Monte Carlo Simulations

[André Assunção S. T. Ribeiro]

Hi Michael,

Besides the CRA moves, I had earlier implemented simple moves for rigid body motion and internal coordinate displacement. I remember Rene Pool was also doing GCMC. So, finding a way to put this all together would be a great start.

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> 
Enviadas: Terça-feira, 31 de Janeiro de 2012 23:53
Assunto: Re: [gmx-developers] Monte Carlo Simulations
 
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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