GOMC parsing

Parsers for extracting alchemical data from GOMC output files.

The parsers featured in this module are constructed to properly parse GOMC free energy output files, containing the Hamiltonian derivatives (\(\frac{dH}{d\lambda}\)) for TI-based estimators and Hamiltonian differences (\(\Delta H\) for all lambda states in the alchemical leg) for FEP-based estimators (BAR/MBAR).

API Reference

This submodule includes these parsing functions:

alchemlyb.parsing.gomc.extract_dHdl(filename, T)

Return gradients dH/dl from a Hamiltonian differences free energy file.

Parameters:

  • filename (str) – Path to free energy file to extract data from.

  • T (float) – Temperature in Kelvin at which the simulation was sampled.

Returns:

dH/dl – dH/dl as a function of step 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.gomc.extract_u_nk(filename, T)

Return reduced potentials u_nk from a Hamiltonian differences dat file.

Parameters:

  • filename (str) – Path to free energy file to extract data from.

  • T (float) – Temperature in Kelvin at which the simulation was sampled.

Returns:

u_nk – Potential energy 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.gomc.extract(filename, T)

Return reduced potentials u_nk and gradients dH/dl from a Hamiltonian differences free energy file.

Parameters:

  • xvg (str) – Path to free energy file to extract data from.

  • T (float) – Temperature in Kelvin the simulations sampled.

  • filter (bool) – Filter out the lines that cannot be parsed. Such as rows with incorrect number of Columns and incorrectly formatted numbers (e.g. 123.45.67, nan or -).

Returns:

A dictionary with keys of ‘u_nk’, which is a pandas DataFrame of potential energy 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.