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

Gianluca Interlandi gianluca at u.washington.edu
Tue Jan 24 03:36:25 CET 2012

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?


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> 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
>                          +1 (206) 685 4435
>                          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
                     +1 (206) 685 4435

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

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