Free energy profiles in ABF tutorial

From: Haleh a (
Date: Mon Nov 16 2015 - 06:35:30 CST

Dear NAMD users,

I have a question regarding the tutorial on Adaptive Biasing Force
Calculations in NAMD. Could anyone help me to understand how figures 1, 5
and 8 on free energy profiles were obtained? I know that integrating the
PMF profiles gives me the reversible work necessary for the reaction.
However, it is unclear how these free energy profiles were plotted based on
the ABF simulation outputs.

Many thanks,
Haleh Abdi

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