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

Rodrigo Faccioli rodrigo_faccioli at uol.com.br
Tue Jan 24 03:32:50 CET 2012


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

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
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<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/<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/<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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