Ok, Thank you once again. On Wed, May 30, 2012 at 4:20 PM, Justin A. Lemkul <[email protected]> wrote:
> > > On 5/30/12 9:17 AM, Nitin Agrawal wrote: > >> I got this by using the command : >> >> g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o >> profile_new1.xvg -hist histo_new1.xvg -unit kCal >> >> is their any way to shift the 0 in the y axis so it corresponds to -2 in >> the >> x-axis. It is just to make the graph look neater and the calculations to >> become >> easier >> >> > That's precisely what your command is doing. > > The data in the PMF curve are dependent upon how the umbrella sampling > calculations were conducted. There is no way to manipulate the positions > of values along the curve, nor should you want to. The -zprof0 option > simply allows you to choose a convenient reference point, since free energy > is calculated as the difference between two states. Any further > manipulation would be spurious. > > -Justin > > >> On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul <[email protected] >> <mailto:[email protected]>> wrote: >> >> >> >> On 5/30/12 8:57 AM, Nitin Agrawal wrote: >> >> How can I define the value at y axis then? Is there any way to >> bring the >> y-axis >> value down to 0? >> >> >> You want the energy minimum to be equal to zero, correct? This is >> nothing >> more than a reference point, so the value passed to -zprof0 is the >> coordinate value (x-axis) at which the energy minimum occurs. Setting >> a >> proper value will shift the curve such that the energy minimum is at >> zero. >> >> -Justin >> >> On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: >> >> >> >> On 5/30/12 8:18 AM, Nitin Agrawal wrote: >> >> When I am using the command -zprof0. it is not giving the >> desired >> result. I am >> using it as >> >> g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if >> pullf_files.dat -o >> profile_new1.xvg -hist histo_new1.xvg -unit kCal >> >> but the lowest point in the graph is still -6.0 in the y >> axis >> and not >> set to 0.0 >> >> Am i using the parameters wrong? >> >> >> >From g_wham -h: >> >> "-zprof0 real 0 Define profile to 0.0 at this position >> (with -log)" >> >> The value provided should be the point along the x-axis (the >> reaction >> coordinate) where you want the value of the PMF (on the >> y-axis) to >> be zero. >> Your original plot only contained values between about -2 and >> 2, so >> specifying -6 is not valid. >> >> -Justin >> >> On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal >> <[email protected] >> <mailto:nitinyugalagrawal@**gmail.com<[email protected]> >> > >> <mailto:nitinyugalagrawal@__gm**ail.com <http://gmail.com><mailto: >> nitinyugalagrawal@**gmail.com <[email protected]>>> >> <mailto:nitinyugalagrawal@ <mailto:nitinyugalagrawal@>__g** >> m__ail.com <http://gm__ail.com> >> <http://gmail.com> >> >> >> <mailto:nitinyugalagrawal@__gm**ail.com <http://gmail.com> >> <mailto:nitinyugalagrawal@**gmail.com<[email protected]>>>>> >> wrote: >> >> Thank you >> >> >> On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> <mailto: >> [email protected] >> <mailto:[email protected]>>>> wrote: >> >> >> >> On 5/30/12 6:29 AM, Nitin Agrawal wrote: >> >> Hi all, >> >> I want to set the lowest point in my curve as >> zero >> instead of >> negative number. >> Can anyone tell me which option to use to do >> that? >> >> >> Set the desired value with -zprof0. >> >> -Justin >> >> -- >> ==============================**______========== >> >> >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> >> <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**____vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> >> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> > >> >> <http://vt.edu/Pages/Personal/**__justin<http://vt.edu/Pages/Personal/__justin> >> >> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> >> >> >> >> <http://www.bevanlab.biochem._**___vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> >> <http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >>**> >> >> ==============================**______========== >> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>**> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[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> >> > >> >> >> <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> >> >> >> >> >> >> <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> >> > >> >> <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> >> > >> >> >> <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> >> >> >> >> >> >> <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> >> > >> >> <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]> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >> >> <mailto:gmx-users-request@ <mailto:gmx-users-request@>__g** >> r__omacs.org <http://gr__omacs.org> >> <http://gromacs.org> >> >> >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <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> >> > >> >> >> <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> >> >> >> >> >> >> <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> >> > >> >> <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> >> >>> >> >> >> >> >> -- >> Regards, >> Nitin Agrawal, >> Master's Student (Bioinformatics) >> University of Turku,Finland >> B.Tech (Biotechnology) >> National Institute of Technology,Durgapur,India >> Blog:http://____**notjustanyotherblog.blogspot._** >> ___com/ >> >> <http://notjustanyotherblog.__**blogspot.com/<http://blogspot.com/> >> >> >> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/> >> >> >> >> >> >> >> -- >> Regards, >> Nitin Agrawal, >> Master's Student (Bioinformatics) >> University of Turku,Finland >> B.Tech (Biotechnology) >> National Institute of Technology,Durgapur,India >> Blog:http://____**notjustanyotherblog.blogspot._**___com/ >> <http://notjustanyotherblog.__**blogspot.com/<http://blogspot.com/> >> >> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/> >> >> >> >> >> >> >> -- >> ==============================**____========== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin >> >> <http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> >> >> ==============================**____========== >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> <mailto:[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> >> > >> >> <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> >> > >> >> <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]> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <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> >> > >> >> <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> >> >> >> >> >> >> >> -- >> Regards, >> Nitin Agrawal, >> Master's Student (Bioinformatics) >> University of Turku,Finland >> B.Tech (Biotechnology) >> National Institute of Technology,Durgapur,India >> Blog:http://__**notjustanyotherblog.blogspot._**_com/ >> >> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/> >> > >> >> >> -- >> ==============================**__========== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> 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> >> > >> >> >> >> >> -- >> Regards, >> Nitin Agrawal, >> Master's Student (Bioinformatics) >> University of Turku,Finland >> B.Tech (Biotechnology) >> National Institute of Technology,Durgapur,India >> Blog:http://**notjustanyotherblog.blogspot.**com/<http://notjustanyotherblog.blogspot.com/> >> > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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> > -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
