Create Analysis Module

[ehhartmann]

• improve trajectory concatenating tool to get meaningful trajectories based on KMC scheme
• graph/vmd visualisation of population of radical positions in the molecule
• graph/vmd visualisation of radical flux from each position
• graph/vmd visualisation of most probable radical migration pathways
• analysis of racemization
• plot energy profile over simulation (of protein only)

[ehhartmann]

• trjcat
  • acts on the run directory and can search for md simulations that get concatenated
• energy profile
  • acts on md.edr files to create xvg files to create plots over the whole run, x axis == frame?
• radical analyses
  • underlying representation: graph or molstar with b-factor based coloring
  • population analysis should work fine. write radical position as info in the log? -> act on kimmdy.log
  • flux analysis should be fine, visualization difficult
  • migration pathway analysis more involved
  • racemization analysis more involved, should not be default kimmdy analysis tool

I think all would be postprocessing tools

[KRiedmiller]

In #158 I started already for the reaction rates. Idea was not so much post processing, but optional live analysis per kimmdy step.
I think we can reuse this for the post-run analysis in this module.

[jmbuhr]

live analysis is pretty sweet!

[ehhartmann]

I would implement the radical population analysis tomorrow and then leave it at that. Feel free to change or add to any part of this module.

[ehhartmann]

Current state of the analysis:
-trjcat works just fine as far as I can see

• plot_energy gets ugly for longer kimmdy runs and plotting some energies together doesn't make sense (e.g total energy of -5000 and bond energy of 100 kj/mol)
• radical_population can analyze one or multiple runs together and returns a plot and a pdb with fractional occupancy as beta column. I think this is fine for now