NAMD parsing¶
Parsers for extracting alchemical data from NAMD output files.
The parsers featured in this module are constructed to properly parse NAMD .fepout output files containing derivatives of the Hamiltonian and FEP (BAR) data.
See the NAMD documentation for the theoretical backdrop and implementation details.
If you wish to use BAR on FEP data, be sure to provide the .fepout file from both the forward and reverse transformations.
After calling extract_u_nk() on the forward and reverse work values, these dataframes can be combined into one:
# replace zeroes in initial dataframe with nan
u_nk_fwd.replace(0, np.nan, inplace=True)
# replace the nan values with the reverse dataframe --
# this should not overwrite any of the fwd work values
u_nk_fwd[u_nk_fwd.isnull()] = u_nk_rev
# replace remaining nan values back to zero
u_nk_fwd.replace(np.nan, 0, inplace=True)
# sort final dataframe by `fep-lambda` (as opposed to `timestep`)
u_nk = u_nk_fwd.sort_index(level=u_nk_fwd.index.names[1:])
The fep-lambda index states at which lambda this particular frame was sampled, whereas the columns are the evaluations of the Hamiltonian (or the potential energy U) at other lambdas (sometimes called “foreign lambdas”).
API Reference¶
This submodule includes these parsing functions:
- alchemlyb.parsing.namd.extract_u_nk(fep_file, T)¶
Return reduced potentials u_nk from NAMD fepout file.