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 < gianl...@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 gianl...@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. > ------------------------------**----------------------- > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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