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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Sep 17 2020 - 14:42:53 CDT

The output should look something like this:

colvars: Restraint harmonic1, stage 0 : lambda = 0
colvars: Setting force constant to xxxxx
.... (steps)
*colvars: Lambda= 0 dA/dLambda= -0.0195425*
colvars: Restraint harmonic1, stage 1 : lambda = 0.25
colvars: Setting force constant to xxxx
.... (steps)

On Thu, Sep 17, 2020 at 2:20 PM Faisal, H M Nasrullah <
hmnasrullah.faisal_at_ndsu.edu> wrote:

> Hi Giacomo,
>
> Thanks for your reply. But I cannot see any free energy difference in my
> log file. I am using NAMD 2.12.
>
> Thanks
> Faisal
>
> ------------------------------
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Thursday, September 17, 2020 10:40 AM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>; Faisal, H M Nasrullah <
> hmnasrullah.faisal_at_ndsu.edu>
> *Subject:* Re: namd-l: Output of harmonic restrains effect in alchemical
> route of protein-ligand binding free energy calculation
>
> 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
>

-- 
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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