From: Chris Goedde (chris.goedde_at_gmail.com)
Date: Wed Dec 14 2016 - 13:13:01 CST
Couple of questions.
How are the energies reported in the NAMD log file computed? The bonded energies are pretty obvious; I’m 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 doesn’t seem to be a sum of other energies, that I can tell …
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