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> 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> 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? 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