[gmx-users] Re: boundaries in PMF

Justin A. Lemkul jalemkul at vt.edu
Thu May 31 21:52:48 CEST 2012

On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
> OK,
> however, just one point about your last comment:
>  > I suspect this is why g_wham is finding a range of values only equal to half of
>  > your expected reaction coordinate; it is considering only the positive
>  > displacement along the reaction coordinate.
> It seems like all the channel is explored, not only one half. If g_wham was only
> considering the positive displacement I should see a profile for just one half
> of the channel, shouldn´t I? and I can see a profile typical for the entire channel.

Then perhaps it's just a small g_wham output bug (boundary values).  You didn't 
mention that your profile looked normal ;)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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