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
- 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
- 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.