RE: NAMD Energies

From: Radak, Brian K (
Date: Wed Dec 14 2016 - 13:42:36 CST

The log output is the energies used in the simulation - all terms and cutoffs. PME counts as ELECT and LJcorrections count as VDW.

The energy plugin might make certain fixed assumptions on the cutoffs, etc. that don't match your simulation settings. If memory serves, you can save the NAMD input file that the plugin uses and compare the settings. I can't think of any particular reason why you shouldn't be able to match to at least 2-3 decimal places with the same settings.

I have no idea what the conformational energy output does - I'd expect this is documented with the plugin? You might also be able to infer from the NAMD input file that is used if you can get your hands on it.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

From: [] on behalf of Chris Goedde []
Sent: Wednesday, December 14, 2016 1:13 PM
Subject: namd-l: NAMD Energies

Hi all,

Couple of questions.

How are the energies reported in the NAMD log file computed? The bonded energies are pretty obvious; Iím wondering more about the electrostatics and VdW. In particular, are the values for cutoff, pairlistdist, etc. used, or is the full energy of all interactions calculated? If PME is on, does that affect the electrostatic energy calculation?

Second question. When I use the NAMD Energy plugin in VMD on a dcd file, the electrostatic energy is a bit different from that reported in the namd log file (about 10% different). What could be the cause of this? Also, what goes into the conformational energy reported by this plugin? It doesnít seem to be a sum of other energies, that I can tell Ö



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