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. Shahid Nayeem On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem <msnay...@gmail.com> 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. > Shahid Nayeem > > On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <jalem...@vt.edu> 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 | (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> >> > >
profile.xvg
Description: Binary data
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