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.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 ===================================================== ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Rodrigo Faccioli [rodrigo_facci...@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_facci...@uol.com.br<mailto:rodrigo_facci...@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 <gianl...@u.washington.edu<mailto:gianl...@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 <gianl...@u.washington.edu<mailto: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 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 gianl...@u.washington.edu<mailto:gianl...@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. ----------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------------- Gianluca Interlandi, PhD gianl...@u.washington.edu<mailto:gianl...@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. ----------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
