From: Mark Triger (mark.t.triger_at_gmail.com)
Date: Wed Jun 27 2012 - 13:19:48 CDT
I've been running some simulations using the External Electric Field
functionality of NAMD.
For various reasons, I would like to perform analysis of the energies in my
simulation afterwards, using NAMD to step through my DCD files with 'run 0'.
However, when I look at the component of the energy output that comes from
the external electric field (in the MISC column), I am unable to reporduce
it. Here is the energy output, for the same step of the same simulation,
from the original output log and from post-hoc analysis with 'run 0'. I am
specifying the same external electric field vector in both scripts.
========
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL
TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
#original run
ENERGY: 1000 3981.1472 21458.8269 14106.4023 222.0955 -209035.8017
5013.3230 0.0000 4.1355 55476.8249 -108773.0465 308.4144 -164249.8714
-108383.0008 308.3814 -45.5994 -48.6250 812451.0224 -22.9624 -23.6279
# and post-hoc
ENERGY: 1000 3981.1458 21458.8256 14106.4023 222.0959 -209035.8098
5013.3318 0.0000 8.7539 0.0000 -164245.2546 0.0000 -164245.2546
-163865.3547 0.0000 -1602.7986 -1623.6146 812451.0018 -1602.7986 -1623.6146
======
As you can see, the BOND, ANGLE, DIHED, IMPRP, ELECT, & VDW columns are
all basically exactly unchanged, as expected. But the MISC column that
reports the external efield energy almost doubles from 4.1355 to 8.7539.
What might be causing this? Is there a way to get the external electric
field energies correct post-hoc?
Thanks!
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