efield energies incorrect in analysis mode (run 0) ?

From: Mark Triger (mark.t.triger_at_gmail.com)
Date: Wed Jun 27 2012 - 16:25:04 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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