a3fe.analyse.mbar

Functionality for running mbar on SOMD output files. This uses pymbar through SOMD

Functions

collect_mbar_slurm(output_dir, run_nos, ...)

Collect the results from MBAR slurm jobs.

run_mbar(output_dir, run_nos[, ...])

Run MBAR on SOMD output files.

submit_mbar_slurm(output_dir, virtual_queue, ...)

Submit slurm jobs to run MBAR on SOMD output files.
a3fe.analyse.mbar.run_mbar(output_dir: str, run_nos: List[int], percentage_end: float = 100, percentage_start: float = 0, subsampling: bool = False, delete_outfiles: bool = False, equilibrated: bool = True) → Tuple[ndarray, ndarray, List[str], Dict[str, Dict[str, ndarray]]][source]

Run MBAR on SOMD output files.

Parameters:

  • output_dir (str) – The path to the output directory

  • run_nos (List[int]) – The run numbers to use for MBAR.

  • percentage_end (float, Optional, default: 100) – The percentage of data after which to truncate the datafiles. For example, if 100, the full datafile will be used. If 50, only the first 50% of the data will be used.

  • percentage_start (float, Optional, default: 0) – The percentage of data before which to truncate the datafiles. For example, if 0, the full datafile will be used. If 50, only the last 50% of the data will be used.

  • subsampling (bool, Optional, default: False) – Whether to use subsampling for MBAR.

  • delete_outfiles (bool, Optional, default: False) – Whether to delete the MBAR analysis output files after the free energy change and errors have been extracted.

  • equilibrated (bool, Optional, default: True) – Whether to use the equilibrated datafiles or the full datafiles. If true, the files name simfile_equilibrated.dat will be used, otherwise simfile.dat will be used.

Returns:

  • free_energies (np.ndarray) – The free energies from each run, in kcal mol-1.

  • errors (np.ndarray) – The mbar errors on the free energies from each run, in kcal mol-1.

  • mbar_out_files (List[str]) – The paths to the MBAR output files.

  • mbar_grads (Dict[str, Dict[str, np.ndarray]]) – The gradients of the free energies obtained from the MBAR results (not TI), for each run.