NAMD Energy types

From: Lada Biedermannová (
Date: Wed Sep 08 2010 - 04:16:30 CDT

Hi all,

I am using the NAMD Energy plugin to get internal energies of a
selection of my system. However, I am confused by the fact that I am
getting a non-zero Bond, Angle and Dihed energies even for a selection
of two atoms that are not bonded, eg. for two CB atoms as shown below.
Could somebody explain where these numbers come from?


Lada Biedermannova

namdEnergy) Computing energy for selection:
namdEnergy) index 6 16

namdEnergy) Running:
namdEnergy) /sw/mcm/app/namd/NAMD_2.6_Linux-i686/namd2 namd-temp.namd

Frame Time Bond Angle Dihed
Impr Elec VdW Conf Nonbond
0 0 +0.1559 +0.0737 +1.1857
+0 -0.9343 -0.0181 +1.4153 -0.9524

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