From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_force_k_ti
Is this showing up in your runs? If not, what is the version of NAMD that
you are using?
Giacomo
On Thu, Sep 17, 2020 at 11:09 AM Faisal, H M Nasrullah <
hmnasrullah.faisal_at_ndsu.edu> 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 http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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