Add a routine to calculate and output instantaneous kinetic temperature.

[naotohori]

To check the consistency with the pre-defined system temperature.

This must be straightforward.

[naotohori]

Did some tests to see deviations of kinetic temperature from the system temperature.

The results are summarized in https://github.com/naotohori/MDcode/blob/master/integrator_test/Temperature_check/Temperature_check.ipynb

• UUUU tetraloop. 2013 model, Honeycutt's Langevin scheme, 10M steps, save=1, viscosity = 0.00001 or 0.000015

  • System temperature set to 300 K
  • Larger deviation (~284 K) when dt = 0.05.
  • Smaller deviation when smaller step size used, ~299 K when dt = 0.001

• Azoarcus folded state, 5 mM Mg, 12 mM KCl, 2015 model, Honeycutt's Langevin, 100k steps, save=10

  • System temperature set to 310 K
  • random seed 1: 309.19 K
  • random seed 2: 310.27 K

The larger deviations for UUUU because of the small system size? It looks okay for azoarcus ribozyme with explicit ions.