Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation

From: Giacomo Fiorin (
Date: Thu Sep 17 2020 - 10:40:50 CDT

Hi Faisal, although the free-energy of a vanishing harmonic restraint is
computed in Colvars, it does not represent a transformation along a
geometric variable, so there is no PMF. Rather, there is a single
free-energy difference between initial and final states being printed out
in the standard output:

Is this showing up in your runs? If not, what is the version of NAMD that
you are using?


On Thu, Sep 17, 2020 at 11:09 AM Faisal, H M Nasrullah <> wrote:

> Hi All,
> I am going over the tutorial of protein-ligand binding free energy
> calculation using the alchemical route. Double annihilation of ligand using
> fep was understandable to me. But I cannot understand the simulation output
> of harmonic restraints' effect on free energy using colvars module. I ran
> the input files of
> 'tutorial-protein-ligand\Archives\AlchemicalRoute\Restraints%3ABound' this
> folder and the output files were .dcd, .log and .colvars.sate file. No .pmf
> file was generated. Then How can I calculate the free energy due to
> harmonic restraints? Any advice will be highly appreciated.
> Thanks
> Faisal

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD

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