tfep.utils.plumed.sumhills.run_plumed_sum_hills

tfep.utils.plumed.sumhills.run_plumed_sum_hills(metad_file_path, output_file_path=None, stride=None, min_to_zero=None, cv_min=None, cv_max=None, n_bins=None, overwrite=False, create_time_file=True)[source]

Run the plumed sum_hills command.

Parameters:

metad_file_path (str) – The path to the file defined in the ‘METAD’ action of the PLUMED script where the hills are saved. Corresponds to the ‘–hills’ option in the plumed sum_hills program.
output_file_path (str, optional) – The path to the output file with the free energy surface. By default, the function generates a fes.dat file in the same directory as the metad file or, if stride is passed, all the files for each stride are saved in a sub directory called ‘fes’.
min_to_zero (bool, optional) – If True, the minimum free energy will be shifted to zero. The default is identical to the program.
stride (int, optional) – If given, the free energy surface is estimated every stride Gaussian depositions. The default is identical to the program.
cv_min (float, optional) – The minimum value of the CV for the grid. It corresponds to the –min option. The default is identical to the program.
cv_max (float, optional) – The maximum value of the CV for the grid. It corresponds to the –max option. The default is identical to the program.
n_bins (int, optional) – The number of bins in the grid used to represent the free energy surface. The default is identical to the program.
overwrite (bool or ‘warning’, optional) – If the output file exist, if True, the output file is overwritten; If False an exception is raised; If the string ‘warning’, the file is not overwritten, but only a warning is raised; If the string ‘ignore’, the output file is not overwritten and the function returns silently.
create_time_file (bool, optional) – By default, when stride is passed, the function creates an extra ‘fes_time.dat’ file with a single column with the time of each ‘fes.dat’ file. Set this to False to turn off this feature.