[gmx-users] Details about using g_wham

[Dr. Vitaly Chaban]

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
> 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
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