Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 10000 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it.
Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul <[email protected]> wrote: > > > shahid nayeem wrote: > >> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling >> was done. The umbrella pullcode used is as follows. >> ; Pull code >> pull = umbrella >> pull_geometry = distance ; simple distance increase pull_dim = >> Y N Y >> pull_vec1 = 0.75 0 1 >> pull_start = yes ; define initial COM distance > 0 >> pull_ngroups = 1 >> pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = >> 0.01 ; 0.01 nm per ps = 10 nm per ns >> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >> >> Please tell me my profile.xvg and histo.xvg are fine or not. In >> profile.xvg why i am not getting smooth convergence. >> > > They're not terrible, but could be better. The PMF profile is a little > rough and there are some regions of the reaction coordinate with little > sampling. Maybe your simulations need to be longer and/or you need to > exclude some amount of time at the beginning of each as equilibration > (which you probably should do anyway, but without seeing your g_wham > command, there's no way to know what you may or may not be considering). > > -Justin > > Shahid Nayeem >> >> >> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> shahid nayeem wrote: >> >> 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 >> >> >> I will have to assume you mean nm. Gromacs does not deal in >> Angstrom, and these distances would be within any sensible >> short-range cutoff and thus not indicative of actual separation. >> >> >> 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. >> >> >> Sorry, I don't have a photographic memory, nor can I recall if >> you've ever posted your .mdp file, or at the very least, told us how >> much sampling you've done in each window. It may well be that your >> simulations are simply too short to observe adequate >> post-equilibration sampling. >> >> >> -Justin >> >> -- ==============================**__========== >> >> >> 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 [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> 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 [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> >
profile.xvg
Description: Binary data
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