Trajectory analysis

A MD simulation performed with the metafalcon package produces a dynamics-0.log file that contains the main results. Every restart will increase the fileindex by one, so that previous results won’t get overwritten. For every dynamics step, coordinates, velocities, energies and other metadata are saved that can be analyzed afterwards.

Run

metaFALCON log2xyz

to extract a file dynamics.xyz that contains the coordinates along the trajectory in a format able to be opened in most molecular visualization programs. You can change start and end points as well as specify the step size. For details, use the –help option.

Bond lengths, bond angles, torsion angles, coordination numbers and energetic properties can be extracted using the analyze_trajectory class:

from metafalcon.analysis.analyze import analyze_trajectory
anl = analyze_trajectory()

In order to analyze the two bond lengths between the first and the second / third atom, run:

anl.add_property("bond", atoms=[0, 1])
anl.add_property("bond", atoms=[0, 2])

A full description of all possible properties to be analyzed can be found in the documentation of the add_property() method documentation. All added properties will be saved in the meta-config.json file and you can review the list of current analysis properties with:

print(anl.get_properties())

If you want to remove an element from the list, do

anl.remove_property("bond", atoms=[0, 1])

or

anl.remove_property("bond")

for removing all bond lengths. The whole list can be resetted with reset_properties(). If not the whole dynamics trajectory should be analyzed to save computation time, the start, end and stride attributes can be set by the respective setter functions.

anl.set_start(200)
anl.set_end(500)
anl.set_stride(20)

will analyze every 20th time step from step 200 to step 500.

Finally, you can run the analysis with:

anl.analyze()

This run will producte a analyze_*.dat file for every analyzed property.

If you only want to analyze the properties that are already specified in the meta-config.json file, use the command line tool:

metaFALCON analyze