Re: Average energy in NAMD

From: Axel Kohlmeyer (
Date: Sun Jun 01 2008 - 19:22:51 CDT

On Sun, 1 Jun 2008, JC Gumbart wrote:

JCG> You could use NAMD Energy to output the relevant values to a file and then
JCG> use any of a variety of scripting methods (tcl, perl, awk, etc.) to average
JCG> them, or even a program like Excel.

doesn't "namdenergy" run NAMD again?
so why not parse and average the log directly?


JCG> See here:
JCG> On Jun 1, 2008, at 4:31 PM, feng jack wrote:
JCG> >Hi, all,
JCG> > I am new NAMD guy. I have some questiones about average energy:
JCG> > There are three energy items in the standard output files: TOTAL,
JCG> >and TOTAL3, it seems that all of them are current energy rather than
JCG> >average
JCG> >energy. How can I obtain the average energy (e.g, if I want to obtain the
JCG> >average energy in the last 200000 steps)?
JCG> > Thank you for your patient.
JCG> >
JCG> > Best,
JCG> > Jack
JCG> >
JCG> >

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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