mdtraj.dipole_moments

mdtraj.dipole_moments(traj, charges)

Calculate the dipole moments of each frame in a trajectory.

Parameters

trajTrajectory

An mdtraj trajectory.

chargesnp.ndarray, shape=(n_atoms), dtype=float

Charges of each atom in the trajectory, expressed in units of the elementary charge constant.

Returns

momentsnp.ndarray, shape=(n_frames, 3), dtype=float

Dipole moments of trajectory, units of nm * elementary charge.

Notes

This code works by first calculating displacements relative to the first atom in each residue (e.g. local frame). Then, this is added to the PBC-corrected displacement between the first atom in the two molecules. This total displacement is then used as to calculate the box dipole moment.