Hello,
I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer.
I am following the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
and I have a doubt:
In this tutorial the generation of configurations is done using a .mdp file for
pulling one chain from another, but is it possible to generate the
configurations for Umbrella Sampling "by hand", I mean, changing the z
coordinate of the monomer I want to move, then solvating and then minimizing
these configurations? Is there any problem with this protocol for the obtaining
of the configurations?
Thanks a lot for your help.
Best wishes,
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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