On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> Dear Justin and Gmx Users, >> I extracted 42 frames from my trajctory of pulling ligand away from my >> protein (no position restarined). I would like to run NPT before running >> umbrella sampling simulations. As far I see Justin in his tutorial NPT and >> umbrella sampling mdp files looks the same which means you did not restrain >> whole protein in your system during NPT? Why? >> > > The system at hand was very robust and as such, complete restraints were > not necessary. Please do not adhere strictly to the umbrella sampling > tutorial; there are elements of it that may not be generally applicable > (and I'm fairly sure there are warnings of this in the tutorial). It is a > simple example designed to provide the conceptual and practical basis for > such simulations. > > > Shall rund NPT withou restraining protein and ligand before umbrella >> sampling in each window? >> >> > > Do what makes sense in your case. Typically, position restraints are > applied during equilibration. > > -Justin > Maybe I asked my qestion not directly. Why during the equilibration of your system (tutorial) NPT before umbrella sampling in each window you restarined only Chain B like in further umbrella samplin (your mdp files of NPT and MD are the same) instead of restraining all chains as it should be during the equilibration? Steven > > -- > ==============================**========== > > 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> >
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