Justin, Could you tell me if I want to simulate self-organization of the pure lipid bilayer starting from the initial random placed molecules in water. Does this simulation need in pre-md NVT and NPT equilibration? What the average time for NPT? I think that If this stage should occur it must be consist of long ( tens of NS ) preequilibration.
James 2011/10/21 Justin A. Lemkul <jalem...@vt.edu> > > > > You'll learn far more by discovering it yourself. >> > > I stand by this statement. Perhaps some kind person with sufficient time > on their hands will do your literature searching for you, but I do not, > sorry. The information you need is out there. Start with the primary > citation for whatever force field you want and search databases for citing > articles or check out the references therein. Even Google can pull up very > useful results within seconds, provided you've given sufficiently specific > keywords. > > -Justin > > >> >> That's why at the present moment I'm examining different force fields and >> their implementation to the different systems. Could you recomend me some >> survey arcticle when I could find something usefull for this ? In >> particular I wounder to know about parametrisation for the membrane systems? >> Previosly I've found that charmm ff is ,ost accurasy in the case of such >> examination but I've not been able to rapametrise my bilayers via this ff >> yet ;x >> On other hand I have not difficulties with GROMOS ff for different systems >> ( e.g I've obtained very stabile systems durins some ns of simulations but I >> dont know about accuracy of the parametrisation of this ff in the case of >> membrane system for example . >> >> Finally I'm looking for tutorial for simulation of the pure lipids. E.g I >> want to simulate of different physical events on my membrane ( e.g I want to >> overkill my membrane by hyperpolarisation or other electrostatic effects >> emerged on the different steps of my simulation ) Could you also recomend me >> methodical literature for this styding? >> >> >> >> James >> >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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
