From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Mon Nov 28 2016 - 08:08:03 CST
Harish,
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
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:50 CST