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

Dallas Warren dallas.warren at monash.edu
Wed Dec 12 23:42:05 CET 2018


Good resource to check is the manual.  I'm pretty sure most of the
calculations performed / formulas used are in there somewhere?  Another
option is in the header text for the script itself, when appropriate there
will be a reference to a paper where the code/formula/method has come from.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Thu, 13 Dec 2018 at 03:12, James <james at ryley.com> wrote:

> Hi!
> 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
> information?
> Sincerely,
> James Ryley
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