Unless you symmetrize the PMF before output, it should be along an entire box side.
You do not specify how you pulled your molecule; therefore, it is impossible to suggest further. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Tue, Jul 29, 2014 at 1:42 AM, Yoo Chan Myung <yucha...@gmail.com> wrote: > Dear GMX-Users, > > I’m trying to obtain free energy profile of small molecule penetration > through POPC membrane. > > To do that, many researchers simulate using Umbrella Sampling with G_Wham > analysis. > > (Reference : 'convergence of free energy profile of coumarin in lipid > bilayer’, Michal Otypeka) > > > Most of x-axis(Distance from the middle of the lipid bilayer) of free > energy profile show minus to plus x-axis. > > In my case, I have no idea how to obtain the g_wham results with region > from minus to plus of membrane(x-axis). > ($ g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal) > > I always get an energy profile which is raged from 0 to 3 for x-axis, not > in minus. > > Is there any options on g_wham? > > Many thanks, > > Yoochan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
