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

[Dallas Warren]

James,

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
nail.


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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