From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Sep 17 2020 - 16:48:19 CDT
Hi Faisal, that's fair: I added a very simple note to the Colvars
documentation, you should be seeing it in the web link that I already sent:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_force_k_ti
For future reference, when you over a NAMD tutorial that uses a lot of
Colvars features you are generally better off also looking the keywords up
in the Colvars manual:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html
https://colvars.github.io/pdf/colvars-refman-namd.pdf
Several of the tutorials from the NAMD website are useful for a first
exposure to a given topic, but they are also quite sloppy when it comes to
pointing the reader to the correct documentation. You often need to look
things up on your own to get complete information (which in this case, was
also made more complete thanks to your feedback).
Giacomo
On Thu, Sep 17, 2020 at 5:07 PM Faisal, H M Nasrullah <
hmnasrullah.faisal_at_ndsu.edu> wrote:
> Hi Giacomo,
>
> Thanks, it worked. I just didn't know what to search.
>
> Regards
> Faisal
>
> ------------------------------
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Thursday, September 17, 2020 2:42 PM
> *To:* Faisal, H M Nasrullah <hmnasrullah.faisal_at_ndsu.edu>
> *Cc:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
> *Subject:* Re: namd-l: Output of harmonic restrains effect in alchemical
> route of protein-ligand binding free energy calculation
>
> 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
>
-- 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
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:14 CST