[gmx-users] Getting more detail than is in the documentation

James james at ryley.com
Wed Dec 12 17:11:58 CET 2018


There are frequently times when I would like a lot more detail on how a
command works than is in the docs. For example, with respect to the "traj"
command option "-ekr", this is all it says:

"Options -ekt and -ekr plot the translational and rotational kinetic energy
of each group..."

But, how is it calculating the numbers? The numbers I get are very low
(e.g., 0-5 kJ/mol) so I am guessing that it subtracts thermal energy. If
so, how does it tell thermal from rotational energy? And how does it
determine the axis of rotation?

That's just an example, but what it boils down to is that it would often be
nice to be sure one understands exactly what number gromacs is giving you,
and the documentation is light on details, formulas, and examples. I could
try reading the code, but I doubt that I would end up with great confidence
in the answer (due to my lack of coding skill, not the code). Does anyone
know of a reference book, or other sources, that might contain such

James Ryley

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