[gmx-users] umbrella sampling

susanta haldar susantahaldar at gmail.com
Sun Sep 21 12:39:40 CEST 2014

Hi all,

  I am running a umbrella sampling simulation. Pulling a lysine residue
near to inhibitor inside a protein. So that I used pull code in 3 dimension
(pull_dim = Y Y Y ). Therefore I got 3 coordinates (dx, dy, dz) in the
pullx-file.xvg. Now I need to run g_wham to calculated the PMF.

   How the WHAM would be working here? How to work with all those 3
coordinates to calculate the Free energy of pulling?
I would be very happy if somebody help me on this regard.

thank you in advanced.

Susanta Haldar
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic.

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