fast_forward.interaction_fit module

functions for fitting interaction distributions

class fast_forward.interaction_fit.InteractionFitter(precision, temperature, constraint_converter, max_dihedrals, dihedral_scaling)[source]

Bases: object

Class to fit interactions

Parameters:

  • precision (int) – precision to round values to for writing

  • temperature (int) – temperature of interaction distribution in boltzmann inversion

  • constraint_converter (int) – threshold above which to convert bonds to constraints

  • max_dihedrals (int) – maximum number of dihedrals to fit proper dihedrals with

property dihedrals
fit_interaction(data, atoms, group_name, inter_type, vs_constructors=[])[source]

Fit an interaction for a group of atoms, and assign the fitted parameters to gromacs variables in self.interactions_dict

Parameters:

  • data (ndarray) – histogram of input data

  • atoms (list) – (lists of) atom indices involved in the given interaction

  • group_name (str) – name of interaction group

  • inter_type (str) – name of interaction type being analysed

  • vs_constructors (list) – indices of atoms which are virtual sites. Cannot construct constraints from virtual sites, so these will be overwritten if found.

fit_to_gmx(inter_type, group_name, atoms, vs_constructors)[source]
interactions_dict: defaultdict