PMF decompostion

From: Azadeh Alavi (
Date: Mon Sep 12 2016 - 06:49:50 CDT

Dear Namd users

I have a membrane-protein system using charmm36 force field and have
calculated the PMF profile for the permeation of an ion across the channel
using the ABF method. I wished to know how to decompose the PMF profile
into individual contributions from the ion’s interactions with its first
solvation shell water (defined as 3.3 A° from sodium for instance), using
pair interaction utility in NAMD. As far as I know, in the this utility, a
file should be prepared in which selected atoms are to be distinguished by
1 and 2 in the B column. However, in order to consider the first solvation
shell water, the file needs to be updated while the .dcd file is being read
and I do not know how it it is possible.

Your help would be greatly appreciated.
Thank you.

Best regards,

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