mmml umbrella-mbar¶
MBAR post-processing for umbrella-sample runs.
Usage¶
mmml umbrella-mbar --help
Options¶
usage: mmml umbrella-mbar [-h] --run-dir RUN_DIR [--checkpoint CHECKPOINT]
[--temperature-K TEMPERATURE_K] [--mbar-verbose]
[--ml-batch-size ML_BATCH_SIZE]
MBAR analysis for a completed umbrella-sample run. Reads umbrella_snapshots.npz
from --run-dir and updates umbrella_summary.json.
Input & configuration:
--checkpoint CHECKPOINT
Override checkpoint for U_ML re-evaluation (default:
from snapshots/summary).
Scientific model:
--temperature-K TEMPERATURE_K
kT for reduced potentials (default: from
snapshots/summary).
Execution:
--ml-batch-size ML_BATCH_SIZE
Reserved for batched U_ML re-eval (default: 32)
Diagnostics & safety:
-h, --help show this help message and exit
--mbar-verbose Verbose pymbar output
Other options:
--run-dir RUN_DIR Output directory from mmml umbrella-sample
CLI for MBAR post-processing of umbrella sampling runs. Usage: mmml umbrella-
mbar --run-dir out/umbrella [--checkpoint PATH] [--temperature-K 300]