Thanks for you prompt reply! Clear and to the point. -Shay On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Shay Teaching wrote: > >> Dear Gromacs Users, >> >> I've done Justin's tutorial regarding PMF/umbrella sampling and now, when >> approaching my own system I have a couple of questions. >> (Link to the tutorial here: http://www.bevanlab.biochem.** >> vt.edu/Pages/Personal/justin/**gmx-tutorials/umbrella/06_**umbrella.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html>) >> >> My system is comprise of a transport protein (embedded in membrane) and a >> ligand. The system is positions so that Z axis is the axis on which I've >> made PMF windows. >> The next step on this is to run these windows separately and I didn't >> quite understand why in step-6 of the tutorial it specifies to still use >> pull_dim = N N Y and pull_rate1 = 0.0. >> >> As far as I understood, during the production run we want to sample the Z >> position. Shouldn't then it use pull_dim = Y Y N ? >> > > No, that would confine the pulled group to the x-y plane, but allow it to > move freely in z. > > > And what does it mean to the system when we set pull_rate1 = 0.0 ? >> > > The harmonic restraint is applied to pull_group1 such that there is no net > change in position. > > > Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains >> pull_group0 on the Z-axis? >> >> > Not pull_group0 (which is the reference group), but pull_group1. > Otherwise, yes. > > -Justin > > > This came a bit longish, >> Thanks in advance, >> >> -Shay >> >> P.S. >> Using Gromacs 4.0.7 >> >> >> >> > -- > ==============================**========== > > 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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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