How can I define the value at y axis then? Is there any way to bring the y-axis value down to 0?
On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <[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]>>> >> wrote: >> >> Thank you >> >> >> On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul <[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> | (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/> >> >> >> >> >> -- >> 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/
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