Grompy looks like fancy. Is it reliable for conducting GCMC?? I also need to perform GCMC along with MD.
In Grompy, it seems that the Grompy is compatible with gromacs 4.0.5. The version of gromacs I use is 4.5.X. Is it possible to use Grompy with my Gromacs?? 2012/1/25 Gianluca Interlandi <gianl...@u.washington.edu> > Hi Renè, > > This might be a silly question. In the documentation of GromPy it says > that: > > "The system consists of mono-atomic water molceules defined in the MARTINI > force field. The intermolecular interactions between such molecules are > modelled using the Lennard-Jones potential only." > > My system is all-atom and all-hydrogen and I need to use the GBSA > solvation model. Is it still going to work, or is the tutorial just an > example of what you can do with GromPy? > > Thanks, > > Gianluca > > > On Tue, 24 Jan 2012, René Pool wrote: > > By the way, the tutorial can be found on the wiki page at >> https://github.com/GromPy/**GromPy/wiki/Tutorial:-Using-** >> GromPy-in-GCMC-mode<https://github.com/GromPy/GromPy/wiki/Tutorial:-Using-GromPy-in-GCMC-mode> >> . >> >> ==============================**======================= >> 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 >> ==============================**======================= >> >> On 01/24/2012 09:30 AM, Pool, R. wrote: >> Hi Gianluca, >> >> You might want to take a look at GromPy >> (https://github.com/GromPy/**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<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 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<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 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<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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