Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. shahid Nayeem
On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: > >> Dear All >> >> I am doing umbrella sampling for a protein complex. After analysis I am >> finding that prifle.xvg has not converged. Now I want to extend simulation. >> I have already pulled one chain to the length of the box. Can I further >> pull by extending the box size and add more windows to umbrella sampling. >> Please suggest. >> > > You would have to use a simple test system to prove that this is a valid > approach. Changing the nature of the system for some windows sounds very > questionable to me, and likely would be to reviewers. > > > How one should ascertain the initial box size so that g_wham gives a >> converged profile.xvg. >> > > You should determine the distance needed to sufficiently separate your > components, that is, determine the minimum COM distance at which > interaction between the two species is negligible. Ideally, they would be > non-interacting, but with PME, that is not possible. > > -Justin > > -- > ==============================**========== > > 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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