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
--
---------------------------------------------------
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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