Re: Free energy profiles in ABF tutorial

From: Giacomo Fiorin (
Date: Mon Nov 16 2015 - 07:52:31 CST

Hello Haleh, the .pmf files will be written automatically in the case of a
1d PMF. With higher dimensionalities, you need to use the external command
abf_integrate, supplied with namd.

On Nov 16, 2015 7:37 AM, "Haleh a" <> wrote:

> 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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