I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. shahid Nayeem
On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > shahid nayeem wrote: > >> Dear Justin >> >> I did some more sampling and sending you profile.xvg, histo.xvg. and >> hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my >> the difference in profile.xvg and hist.xvg. Both should be same but I get >> different curves here. >> >> > I can't tell you the difference because you haven't shown how they were > generated. My blind guess is that hist.xvg (a very confusing name for a PMF > profile) was generated from data that have poor sampling in two regions. > The contents of profile.xvg look normal. I don't know which of these > curves corresponds to histo.xvg, because the histograms therein look fine. > > Please make sure to give full descriptions of these files. You've quote a > message that is over a month old. I've replied to hundreds of messages > since then and I do not remember the full context of our discussion. > > -Justin > > On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> shahid nayeem wrote: >> >> Dear Justin >> I did pmf calculation for my protein-protein complex using your >> tutorial.Off course changing the pull_direction suitable for my >> protein but more or less following the same strategy. I am using >> gromacs_4.5.4 and g_wham utility. The profile.xvg file which I >> get is attached and it shows two dips in PE curve. Please see it >> and tell me why I am getting these dips. >> >> >> You have insufficient sampling in at least these two regions. Your >> histograms should confirm this. >> >> -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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> 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 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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