Thank you very much guys! I will search for some reading. If you can suggest a tutorial I will appreciate.
On Thu, Jan 19, 2012 at 11:57 AM, René Pool <r.p...@vu.nl> wrote: > Hi, > > If I understand the question correctly, you want to know the water > chemical potential in the water/protein/ligand system. > If so, in principle it should be possible to approximate the water > chemical potential using test particle insertion. Gromacs has a utility for > that. > > Cheers, > René > > ==============================**======================= > 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 01/19/2012 02:49 PM, Ivan Gladich wrote: > >> On 01/19/2012 11:34 AM, Steven Neumann wrote: >> >>> Does anyone can help? >>> Dear Gmx Users, >>> I am wondering whether it is possible to obtain in Gromacs chemical >>> potential e.g. of water in the protein - ligand system? >>> Please, advise me to do some further reading, suggest method, maybe >>> tutorial? >>> Thank you, >>> Steven >>> >> Dear Steven >> I am not an expert of protein - ligand system... >> However the chemical potential of a i-th specie is the derivative of the >> potential energy in function of the number of the i-particles present in >> the system. >> As far as I know (and if I am not wrong), in GROMACS the number of >> particle is fixed along all the simulation, i.e., you cannot change the >> number of particles during the simulation. >> Therefore, you cannot simply obtain the chemical potential from one >> single run... >> I suggest you to search in literature; maybe you can combine different >> runs to obtain the chemical potential...but I do not want to say you >> something wrong since I do not have experience in such systems. >> >> Good luck >> Ivan >> >> -- > 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> >
-- 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