From: Faisal, H M Nasrullah (hmnasrullah.faisal_at_ndsu.edu)
Date: Thu Sep 17 2020 - 13:20:05 CDT
Thanks for your reply. But I cannot see any free energy difference in my log file. I am using NAMD 2.12.
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:
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 <hmnasrullah.faisal_at_ndsu.edu<mailto:hmnasrullah.faisal_at_ndsu.edu>> wrote:
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.
-- 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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