[gmx-users] wham analysis

[John Whittaker]

Hi,

>
>  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)

Well, according to this ^ output, the pull coordinate was acting in the z
direction, *and* you were printing the distance between the COM's in the z
direction, not the y direction like you said.

>     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

it appears that you are printing not only just the distance between the
COM's of your groups, but also the pull group coordinates in your output
files.

the WHAM code is telling you that it doesn't expect coordinates in the
pullx file, it only expects the time (in the first column) and the
distance between the COM's calculated from whichever components you chose
in "pull-coord1-dim" (in the second column).

For example, this snippet

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

0.0000  1.74222
0.1000  1.72375
0.2000  1.72106
0.3000  1.71755
0.4000  1.72203
0.5000  1.72997
0.6000  1.71092
0.7000  1.69819
0.8000  1.6921
0.9000  1.70055
1.0000  1.69953
1.1000  1.7005
1.2000  1.69984
1.3000  1.70274
1.4000  1.70807
1.5000  1.71815
1.6000  1.73492
1.7000  1.74009
1.8000  1.76735
1.9000  1.77583
2.0000  1.76892
...

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

You should copy/paste your .mdp file and a snippet of your pullx.xvg
output. It seems like you might have done something different than you
thought.

- John