From: Richard Swenson (
Date: Wed Aug 29 2007 - 10:40:28 CDT


If you want to extract the energy data from your log file and store it into
a new file, you can use the awk program from the command line and redirect
the output to a file.

awk -v timestep=.002 '/ENERGY: / {print $2*timestep" "$12} logfile > ouptut

You can change the $12 to correspond to any term in the energy line (ie. $3
for bond energy, $4 for angle energy, $5 for dihedral energy, and so on).

I hope this is what you wanted,

-----Original Message-----
From: [] On Behalf Of
Philipp Schön
Sent: Wednesday, August 29, 2007 4:47 AM
Subject: vmd-l: VMD analysis using NAMD plot

dear users,
my first question is:
why do namd plot show E(kcal/mol) in the ordinate axis even if i plo
temperature, pressure and so on. is this a bug in vmd or did i screw up my
the second question belongs to the postprocessing in vmd. is it possible to
extract an ascii file containing the time for the x axis and, e.g., the
energy for the y axis, i.e. writing an ascii file with two columns?
thanks in advance
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