Dear all,
I used Justin 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?
I sent message in gromacs comunity , what Justin said:
"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."
I didn't understand it.
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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