mdtraj.compute_rdf¶

mdtraj.compute_rdf(traj, pair_names=None, r_range=None, bin_width=0.005, periodic=True, opt=True)¶

Compute radial distribution functions for pairs in every frame.

Parameters:

traj : Trajectory pair_names : array-like, shape=(2,), optional, default=None Pair of atom names to consider. Atom names are matched using the same regex matching employed by MDTraj’s atom selection DSL. If pair_names is not provided, the RDF will be computed between all atoms. r_range : array-like, shape=(2,), optional, default=(0.0, 1.0) Minimum and maximum radii. bin_width : int, optional, default=0.005 Width of the bins in nanometers. periodic : bool, default=True If periodic is True and the trajectory contains unitcell information, we will compute distances under the minimum image convention. opt : bool, default=True Use an optimized native library to compute the pair wise distances.

Returns:

r : np.ndarray, shape=(np.diff(r_range) / bin_width - 1), dtype=float Radii values corresponding to the centers of the bins. g_r : np.ndarray, shape=(np.diff(r_range) / bin_width - 1), dtype=float Radial distribution function values at r.