[gmx-users] wham analysis

[Justin Lemkul]

On 9/1/19 5:35 AM, Negar Parvizi wrote:
>   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.

I made a guess based on minimal information. You asserted that you 
pulled along y but WHAM indicated the bias was along z. I know that the 
default x-axis label in profile.xvg says "z" and it causes confusion. So 
I provided the comment that I did.

However, it is clear from the gmx wham output below that you did *not* 
apply a bias along y, as you stated:

> File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 dimensions)

This means your reaction coordinate was the z-axis.

> 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)

What happens next? Nothing here says "error," however it looks like your 
input files are of an unexpected format. Perhaps you've switched 
pullx.xvg and pullf.xvg. As someone else suggested, you can use 
pullf.xvg files to get the PMF profile and avoid the issue entirely.

-Justin

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Justin A. Lemkul, Ph.D.
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