[gmx-users] Question about gmx_wham

[John Whittaker]

Hi,

> Hello,
>
> I am currently running Umbrella Sampling simulations on Vitamin E (in
> grommacs version 4.6.5). And I followed the tutorial done by Justin A.
> Lemkul, however I am uncertain of a few things about the gmx_wham command
> that he instructs us to use.
>
> Namely for the two output files, which by default are 'profile.xvg' and
> 'histo.xvg'.
> I was wondering for the profile.xvg file what does the X-axis refer to, as
> it says 'z' in the output file however is that in Angstroms, Nanometers,
> etc.
> The graph I have goes to a value that doesn't make sense in context of my
> simulation (goes to a Z of 70 towards the end which is larger than the
> Z-axis of my simulation  if it was in Angstroms (did it account for
> periodic boundary conditions?)).

The x-axis of profile.xvg is whatever the reaction coordinate was for your
umbrella sampling simulations. The reaction coordinate will change
depending on what system you have and what you're trying to calculate. For
example, in Justin's tutorial the reaction coordinate is the z-axis and
what is outputted (in pullx.xvg) is the distance between the protofibril
and "peptide A" calculated only in the z direction.

You should post the pulling parameters from your .mdp file and describe
what you're trying to learn about your system by doing umbrella sampling.
Otherwise, it's hard to help.

> Secondly I was wondering how to graph the histo.xvg file as I was having
> issues using GNUPLOT, if I shouldn't use GNUPLOT what different graphing
> program should I use?

histo.xvg has many columns, not just 2 like you have from something like a
pullx.xvg file. You're probably not plotting all the columns, but I'm not
sure because you didn't specify what issue you're having.

To get a quick idea of whether or not my histograms are overlapping, I
normally just use Grace with a command like:

xmgrace -nxy histo.xvg

-nxy tells Grace to assume the data file is in X Y1 Y2 Y3 ... format so it
plots all your histograms.


> If there are pages where this information is readily available, please let
> me know and I will use them, however I could not find them so I would like
> your help.
>

maybe the gmx wham paper will be useful:

http://cmb.bio.uni-goettingen.de/pub/Hub_JCTC2010.pdf


> Thank You,
> Alex
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- John