[gmx-users] wham analysis

[Jochen Hub]

Hi,

you can also use the pullf output for WHAM (option -if), this may be easier.

Cheers, Jochen

Am 26.08.19 um 12:59 schrieb Negar Parvizi:
> 
>   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,
> Negar
> 

-- 
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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