Re: A common tool to read the output of NAMD run

From: Richard Overstreet (
Date: Mon Nov 28 2016 - 08:08:03 CST


I usually use a combo of unix commands to compress the output file down
to the energy output. Something like:

grep 'ENERGY: ' <namdoutfile> | sed 's/ENERGY://' | sed 'N;s/\n/ /' | tr
-s " "

Not super elegant but it gets the data down to something I can plot or
average using python. Usually in python I'll load the file into a numpy
array and use something like np.avg(). I would review gnu programs like
the above as well as awk and python.

-Richard Overstreet

On 11/28/2016 07:28 AM, Harish Srinivasan wrote:
> Is there a tool that can read the ASCII data NAMD produces during the
> run ? So that it can help in calculating fluctuations and average over
> a span of time or full simulation for quantities like energy,
> temperature, pressure, potential energy etc.
> Essentially, I want the time data of temperature, total energy,
> potential energy etc. for doing some calculations on my own.
> Thank you,
> Harish

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