RE: Total energy of a residue

From: Brian R Novak (
Date: Tue Jun 23 2009 - 11:03:45 CDT

-----Original Message-----
From: on behalf of Mert Gür
Sent: Tue 6/23/2009 10:08 AM
To: NAMD list
Subject: namd-l: Total energy of a residue
Dear all,
I want to evaluate the internal energy of a residue and the interaction
energy of this residue with the other residues in one step. Would it make
sense to define just the second selection as the whole protein so that I
will end up with the sum of the two mentioned energies.

set sel1 [atomselect top "residue 2"]
set sel2 [atomselect top protein]

 namdenergy -ofile "pe.dat" -all -sel $sel1 $sel2 -par

In case it does not make any sense, I need to define the second selection to
be the whole protein except the selected residue. So that I can evaluate the
energies separately.
How can I do that without writing each residue index separately into the
parenthesis in the second selection?

set sel1 [atomselect top "residue 2"]
set sel2 [atomselect top "whole protein , residue2 excluded"]

I think "protein and not residue 2" should work for sel2

 namdenergy -ofile "pe.dat" -all -sel $sel1 $sel2 -par


NAMDEnergy operates on either one or two selections; if only one selection
is chosen, then internal energies for that selection will be calculated,
whereas if two selections are chosen, only interaction energies between
those selections will be calculated. Selections are given using the standard
VMD atom selection language.

Brian Novak
Postdoctoral Researcher
Mechanical Engineering
Louisiana State University

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