Amber parsing

Parsers for extracting alchemical data from AMBER output files.

Some of the file parsing parts are adapted from alchemical-analysis.

Changed in version 1.0.0: Now raises ValueError when an invalid file is given to the parser. Now raises ValueError when inconsistency in MBAR states/data is found.

The parsers featured in this module are constructed to properly parse Amber MD output files containing derivatives of the Hamiltonian and FEP (BAR/MBAR) data.

API Reference

This submodule includes these parsing functions:

alchemlyb.parsing.amber.extract_dHdl(outfile, T)

Return gradients dH/dl from AMBER TI outputfile.

Parameters:

  • outfile (str) – Path to AMBER .out file to extract data from.

  • T (float) – Temperature in Kelvin at which the simulations were performed

Returns:

dH/dl – dH/dl as a function of time for this lambda window.

Return type:

Series

Changed in version 0.5.0: The scipy.constants is used for parsers instead of the constants used by the corresponding MD engine.

alchemlyb.parsing.amber.extract_u_nk(outfile, T)

Return reduced potentials u_nk from AMBER outputfile.

Parameters:

  • outfile (str) – Path to AMBER .out file to extract data from.

  • T (float) – Temperature in Kelvin at which the simulations were performed; needed to generated the reduced potential (in units of kT)

Returns:

u_nk – Reduced potential for each alchemical state (k) for each frame (n).

Return type:

DataFrame

Changed in version 0.5.0: The scipy.constants is used for parsers instead of the constants used by the corresponding MD engine.

alchemlyb.parsing.amber.extract(outfile, T)

Return reduced potentials u_nk and gradients dH/dl from AMBER outputfile.

Parameters:

  • outfile (str) – Path to AMBER .out file to extract data from.

  • T (float) – Temperature in Kelvin at which the simulations were performed; needed to generated the reduced potential (in units of kT)

Returns:

A dictionary with keys of ‘u_nk’, which is a pandas DataFrame of reduced potentials for each alchemical state (k) for each frame (n), and ‘dHdl’, which is a Series of dH/dl as a function of time for this lambda window.

Return type:

Dict

Added in version 1.0.0.