[gmx-users] Wham analysis

[Justin Lemkul]

On 8/18/19 5:10 AM, Negar Parvizi wrote:
> Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my file which is protein-ligand complex.
> The pulling force was in Y direction. when Umbrella sampling finished, "Wham" couldn't analysis the data because wham is in z direction.what should I do now for wham analysis? how can I change it to Y direction?

WHAM does not presuppose the axis or vector; it does what you tell it. 
If you're referring to the x-axis label in the PMF profile being "z," 
that is just a generic (and perhaps imprecise) label that should be 
changed to the Greek character xi, per conventional notation.

-Justin

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Justin A. Lemkul, Ph.D.
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