NAMD Energy types

From: Lada Biedermannová (lada.biedermannova_at_img.cas.cz)
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?

Thanks,

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
Total
0 0 +0.1559 +0.0737 +1.1857
+0 -0.9343 -0.0181 +1.4153 -0.9524
+0.4629

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