From: Ashar Malik (
Date: Tue Feb 17 2015 - 05:56:18 CST

On Feb 18, 2015 12:46 AM, "Viswanath Pasumarthi" <>
> Hi,
> Since the NAMDEnergy plugin doesn't support evaluation of bonding energies

It does. Please clarify what you mean here?

> Bonding energy plot obtained from NAMD Plot shows
> abnormal behavior in my system and I would like to debug by analyzing
> individual bonding interactions.

Since you think it is not working correctly, maybe you are looking at
something else.

> And when bond energies are calculated with a single atom selection, does
> the plugin
> calculate all the bonding energies that selection is involved in? For
> example, if atom selection is "type OW" in water, it will give total
> bonding energies the OW atom type involves in,

No just the BOND energies not electrostatics not vdw not dihedral not
improper just BOND

> as a function of frame. Is
> that correct?

Yes, you will get a time series ... If you give the NAMDEnergy a trajectory
to process on. If you pass it just one pdb file, just one value will be

Again from the manual,

"In addition to one or two atom selections, the user must also choose one
or more energy types to be calculated. Choices are: bonds, angles,
dihedrals, impropers, vdW energy, electrostatic energy, conformational
energy (bonds, angles, dihedrals, and impropers), nonbond energy (vdW and
electrostatic energy), or all (all other energies). "

So bond will just return the BOND energy which is 1 part of the many
energies that come together to make the total energy.

Hope "this" helps.