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> 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<http://lattes.cnpq.br/1025157978990218> >> Public Profile - >> http://br.linkedin.com/pub/**rodrigo-faccioli/7/589/a5<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> >> >> >> >> >> > ------------------------------**----------------------- > 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 > 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 >
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