mmml lambda-mbar¶
MBAR post-processing for lambda TI.
Usage¶
mmml lambda-mbar --help
Options¶
usage: mmml lambda-mbar [-h] --run-dir RUN_DIR [--checkpoint CHECKPOINT]
[--temperature-K TEMPERATURE_K]
[--couple-residues COUPLE_RESIDUES]
[--ml-cutoff ML_CUTOFF] [--mm-switch-on MM_SWITCH_ON]
[--mm-cutoff MM_CUTOFF] [--mbar-verbose] [--no-plots]
MBAR analysis for a completed lambda-dynamics run. Reads lambda_ti_snapshots.npz
from --run-dir and updates lambda_ti_summary.json.
Input & configuration:
--checkpoint CHECKPOINT
Override checkpoint (default: read from summary args if
present).
--couple-residues COUPLE_RESIDUES
Override 1-based coupled residue numbers (default: read
from snapshots).
Scientific model:
--temperature-K TEMPERATURE_K
kT for reduced potentials (default: from summary or 100
K).
--ml-cutoff ML_CUTOFF
--mm-switch-on MM_SWITCH_ON
--mm-cutoff MM_CUTOFF
Output & artifacts:
--no-plots Skip updating diagnostic plots.
Diagnostics & safety:
-h, --help show this help message and exit
--mbar-verbose
Other options:
--run-dir RUN_DIR Output directory from mmml md-system --setup lambda_ti
or scripts/meoh_dimer_lambda_ti.py