Re: how does NAMD know which residue to (de)couple

From: Michael Robinson (
Date: Sun Jun 21 2020 - 21:26:06 CDT

Hi Qasim,

I would advise looking at the NAMD documentation for running free energy
calculations, in particular this page on the input files:

This page should explain most of the questions you may have about the
unique aspects of the configuration file example you showed above. For
example, the free energy tutorial's .conf file contains the following lines:

alchFile decouple.fep
alchCol B

These lines state that the decoupled residues are detailed in the file
'decouple.fep' (alchFile), and that the information is stored in the
beta column of the file (alchCol). Typically this means any non-0
values in the beta column will select that atom (i.e. to perform the
calculation on the 3rd residue, change the values in the beta column
to 0 for the 1st residue, and to 1 for the 3rd residue). I would like
to emphasise the importance of reading the entire set of information
about free energy methods:

I hope this is helpful,



On Mon, 22 Jun 2020 at 08:34, Qasim Pars <> wrote:

> Dear users,
> Please look the input file in this free energy tutorial:
> How does NAMD know which residue to (de)coupled during the hydration free
> energy calculation? Note that it's the first residue in the tutorial.
> If I want to decouple the third residue in the psf/pdb for the solvation
> free energy calculation, what should I do in the input file? ( that is, I
> want to calculate the solvation free energy of the third residue).
> Any help will be appreciated.
> Thanks,
> --
> Qasim Pars

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