From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Dec 14 2016 - 13:47:16 CST
On Wed, Dec 14, 2016 at 2:13 PM, Chris Goedde <chris.goedde_at_gmail.com>
> Hi all,
> 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 by all interactions you mean, for example, the N*(N-1)/2 possible pairs
of atoms, that behavior is only turned on by fullDirect (off by default):
Most MD simulations will make use of cutoffs to have reasonable throughput
without loss in accuracy.
> If PME is on, does that affect the electrostatic energy calculation?
No, it is meant to only speed up calculations without loss in accuracy
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).
How about the kinetic energy? Velocities are absent in a DCD trajectory
> 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 …
See the brief documentation to the NAMD energy plugin:
If you had read that thoroughly, you would seen the expression
"conformational energy (bonds, angles, dihedrals, and impropers)". Does it
not correspond to the sum of those terms?
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 <%28215%29%20204-4213> Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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