[gmx-users] Details about using g_wham
Dr. Vitaly Chaban
vvchaban at gmail.com
Tue Jul 29 13:00:59 CEST 2014
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 <yuchan.m at 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
> (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,
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users