Amber parsing

Parsers for extracting alchemical data from Amber output files.

Most of the file parsing parts are inherited from alchemical-analysis.

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

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