[gmx-users] Monte Carlo with Gromacs and implicit solvent

Tue Jan 24 09:30:54 CET 2012

Hi Gianluca,

You might want to take a look at GromPy (https://github.com/GromPy/GromPy).
This is a python interface to the GROMACS library. Amongst other applications, there is an option to perform grand-canonical Monte Carlo using GromPy. The necessary energy evaluations are performed using direct library calls to GROMACS. In this way it is possible to get around the possibly prohibitive file I/O in shell implementations that use the GROMACS executables. A paper on GromPy and GromPy/GCMC has recently been accepted in JCC, so more details will follow. In the meantime you can have a look at the code and the tutorial on the above website.

Good luck!

Cheers,
Rene

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

Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-----
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands

Room P 2.75
E: r.pool at vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Rodrigo Faccioli [rodrigo_faccioli at uol.com.br]
Sent: 24 January 2012 05:29
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent

Hi Gianluca,

I forgot to say that the step of compute the energies is considered from pdb2gmx until g_energy.

Sorry about my oblivion.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5

On Tue, Jan 24, 2012 at 1:07 AM, Rodrigo Faccioli <rodrigo_faccioli at uol.com.br<mailto:rodrigo_faccioli at uol.com.br>> wrote:
Hi Gianluca,

Thanks your question.

All steps to obtain a generation with 200 individuals, on average, is 6 minutes for 1VII, example. In each generation I must  converted my proteins Dihedral to Cartesian representation, compute the energies, choose the individuals which will go to reproduction, save previous population. This test was using one core of a conventional Desktop computer.

The proteins, that I have tested my algorithm, vary from 20 to 56 amino acids.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5

On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi <gianluca at u.washington.edu<mailto:gianluca at u.washington.edu>> wrote:
Thanks Enrico!

Just wondering. How fast is it? Calling gromacs must have a lot of overhead. Also, do you call mdrun or does g_energy evaluate the energy?

Gianluca

On Tue, 24 Jan 2012, Rodrigo Faccioli wrote:

Hi,

Although I don't work with MC simulation, I have used Gromacs to obtain energies and others
protein features in my Evolutionary Algorithms (EA).

In general lines, I created a script that calls Gromacs programs and the output of these
programs, such as g_energy (I read its xvg file), I stored it at a specific file which is
read by my algorithm and its values are put into my data structure. I call Gromacs either
implicit or explicit solvent.

My project is working with EA until now. However, the integration with GROMACS is able to
work with other kind of algorithms such as MC. Actually, we have idea to work with MC. But,
I don't know when it will be possible. If you want, we can talk about join these work.

Best regards,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5

On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi <gianluca at u.washington.edu<mailto:gianluca at u.washington.edu>> wrote:
     Hi!

     I would like to use gromacs to perform Monte Carlo simulations in implicit
     solvent of a protein near a surface. The protein is treated as a rigid body
     whereas the surface is fix.

     I see that there are plans to code MC into gromacs:

     http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo

     Is there a preliminary version?

     If not, I wonder whether anybody has tried to do MC with gromacs using IMD and
     MDDriver:

     http://www.baaden.ibpc.fr/projects/mddriver/

     Besides this. Is there an easy way to obtain the force field energy of a system
     using gromacs? Would I have to run a 0-steps MD and read out the energy? I know
     that this would have a big overhead in a MC simulation, but it might be worth
     trying.

     Thanks,

         Gianluca

     -----------------------------------------------------
     Gianluca Interlandi, PhD gianluca at u.washington.edu<mailto:gianluca at u.washington.edu>
                        +1 (206) 685 4435<tel:%2B1%20%28206%29%20685%204435>
                        http://artemide.bioeng.washington.edu/

     Postdoc at the Department of Bioengineering
     at the University of Washington, Seattle WA U.S.A.
     -----------------------------------------------------
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu<mailto:gianluca at u.washington.edu>
                   +1 (206) 685 4435<tel:%2B1%20%28206%29%20685%204435>
                   http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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