mdtraj.compute_rdf

mdtraj.compute_rdf(traj, pairs, r_range=None, bin_width=0.005, n_bins=None, periodic=True, opt=True)[source]

Compute radial distribution functions for pairs in every frame.

Parameters:
  • traj (Trajectory) – Trajectory to compute radial distribution function in.

  • pairs (array-like, shape=(n_pairs, 2), dtype=int) – Each row gives the indices of two atoms.

  • r_range (array-like, shape=(2,), optional, default=(0.0, 1.0)) – Minimum and maximum radii.

  • bin_width (float, optional, default=0.005) – Width of the bins in nanometers.

  • n_bins (int, optional, default=None) –

    The number of bins. If specified, this will override the bin_width

    parameter.

  • 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.

See also

Topology.select_pairs