[gmx-users] boundaries in PMF

Rebeca García Fandiño regafan at hotmail.com
Thu May 31 19:20:28 CEST 2012

I am trying to calculate a PMF for an ion along a channel. Everything went OK, but when I used g_wham I got a profile with strange dimensions for the x-axis.
What are the boundaries g_wham is using for calculating the units of x-axis?

I have used:
g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist file_histo_output.xvg -unit kCal -cycl yes

(version 4.0.7)

and the units I got in the x-axis are determined by the boundaries:

"Determined boundaries to 0.000035 to 2.603290 "

Which are these units? nm?
The z coordinate for my ion explores at least 5 nm!!

I am a bit confused about that. 

Any help will be appreciated.
Thanks a lot for your help in advance!

Best wishes,

Dr.Rebeca Garcia
Santiago de Compostela University
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