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