From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 28 2012 - 00:29:32 CDT
I never used this feature of namd but possibly you should check why your
volume and pressure energy changed that much. Maybe try to also load the
velocities that are part of your end energies anyway and should be there
when you try to reproduce, as I think you didn't loaded them into the run 0
script as the temp is 0.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Mark Triger
> Gesendet: Mittwoch, 27. Juni 2012 23:25
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: efield energies incorrect in analysis mode (run 0) ?
> 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
> #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
> 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?
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