[gmx-users] wham analysis

Negar Parvizi negar.parvizi at yahoo.com
Sun Sep 1 15:49:53 CEST 2019

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?
what justin said: I didn't understand it:
"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."

So I decided copy the error:

Here is the error:

>Found 25 tpr and 25 pull force files in tpr-files.dat and pullf-files.dat, respectively
>Reading 12 tpr and pullf files
>Automatic determination of boundaries...
>Reading file umbrella0.tpr, VERSION 5.1.4 (single precision)
>File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 dimensions)
    Pull group coordinates not expected in pullx files.
    crd 0) k = 1000   position = 0.840198
    Use option -v to see this output for all input tpr files

>Reading pull force file with pull geometry distance and 1 pull dimensions
>Expecting these columns in pull file:
    0 reference columns for each individual pull coordinate
    1 data columns for each pull coordinate
>With 1 pull groups, expect 2 columns (including the time column)
>Reading file umbrella71.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella98.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella111.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella119.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella139.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella146.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella157.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella180.tpr, VERSION 5.1.4 (single precision)
>Reading file umbrella202.tpr, VERSION 5.1.4 (single precision)

I would  appreciate any help
Tanks in advance,


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