From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Nov 28 2016 - 08:34:47 CST
I use the attached simple python script (which uses grep under the hood).
And then I also process the data in python.
On 28 November 2016 at 15:08, Richard Overstreet <roverst_at_g.clemson.edu>
> 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,
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