[gmx-users] Question about gmx_wham

[Alexander Phillips]

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?)).

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?

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.

Thank You,
Alex