mmml plot-restart-velocities¶
Plot |v| distributions and outliers from CHARMM .res files.
Usage¶
mmml plot-restart-velocities --help
Options¶
usage: mmml plot-restart-velocities [-h] [--stem STEM]
[--z-threshold Z_THRESHOLD]
[--output OUTPUT] [--dt-ps DT_PS]
[--no-infer-velocities]
[--max-outliers MAX_OUTLIERS] [--quiet]
directory
Plot |v| distributions from CHARMM restart files (heat.NNNN.res) and flag
velocity outliers.
positional arguments:
directory Directory containing numbered restarts (e.g.
artifacts/md_run2)
Execution:
--dt-ps DT_PS Timestep in ps for coord-delta velocity inference
(default: 0.00025 = 0.25 fs)
Output & artifacts:
--output, -o OUTPUT Write PNG dashboard (default:
<directory>/<stem>_velocity_dashboard.png)
--max-outliers MAX_OUTLIERS
Max outlier rows in Rich summary (default: 20)
Diagnostics & safety:
-h, --help show this help message and exit
--quiet
Other options:
--stem STEM Restart stem for numbered files (default: heat →
heat.0000.res)
--z-threshold Z_THRESHOLD
MAD z-score cutoff for per-atom speed outliers (default:
4)
--no-infer-velocities
Do not infer velocities from consecutive restart
coordinates