Re: [AMBER] Units of summary files produced by process_mdout.perl

From: Jason Swails <>
Date: Mon, 8 Jul 2013 18:36:36 -0400

On Mon, Jul 8, 2013 at 6:13 PM, Hunter Brown <>wrote:

> Hello. Just a quick question. Could someone point me in the direction of
> where to find the units of the numbers in the summary files produced by
> process_mdout.perl. My summary.EPTOT file, seems to have time units of
> picoseconds, and I am not sure what the potential energy units are, but I
> am pretty sure they are NOT kcal/mol. Anyways, some guidance would be
> helpful. I am trying to figure out what how I should label my graphs in
> gnuplot!

The energies _are_ kcal/mol.

Unrelated note: there's another script,, that is a bit
more sophisticated in terms of extracting and plotting data. It lets you
easily select the data you want to plot and plot it directly with a single
click. It also allows you to do some manipulations, like histograms, KDEs,
autocorrelations, etc (and it will also print out a time series dump like does).

It requires a couple extra packages (Tkinter, numpy, and matplotlib -- all
available through your package manager as described on my wiki: In case you were interested.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Jul 08 2013 - 16:00:03 PDT
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