AMBER Archive (2008)

Subject: AMBER: benchmark walltime to ps/day calculation

From: Andrew Ring (aring_at_berkeley.edu)
Date: Thu Jan 31 2008 - 14:11:05 CST

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Hello All,

Could someone provide a simple equation for calculating ps/day from
benchmark results. I am failing to understand the two explanations I
have located.

One post from 2005 (http://amber.ch.ic.ac.uk/archive/200508/0205.html)
on the Amber mailing list contains the equation:
ps per day = total_time * nstlim * dt / 86400
This equation gives me numbers which are unreasonably low and vary
directly with total process time (higher wall time results in higher
ps/day).

Unfortunately, I am missing something important to understanding the
explanation at (http://amber.ch.ic.ac.uk/amber8.bench1.html):
The value of ps per day = 86.4/(seconds per step), for a time step of
1 fs. Double this value if you plan to use 2 fs time steps.

Thank you,
Andrew Ring
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