mdtraj.compute_nematic_order¶

mdtraj.
compute_nematic_order
(traj, indices='chains')¶ Compute the nematic order parameter of a group in every frame.
The nematic order parameter describes the orientational order of a system with a value between 0 and 1. A completely isotropic system, such as a liquid, has no preferred direction and a nematic order parameter of 0. An anisotropic system, such as many liquid crystals, monolayers or bilayers, have a preferred orientation and will have a positive order parameter where a value of 1 signifies perfect ordering.
 Parameters
 trajTrajectory
Trajectory to compute ordering in.
 indices{‘chains’, ‘residues’, list of lists}, optional, default=’chains’
The group to consider. Users can pass their own indices as a list of lists with the “shape” (n_compounds, len(each_compound)). Recognized string keywords are ‘chains’ and ‘residues’.
 Returns
 S2np.ndarray, shape=(traj.n_frames,), dtype=float64
Nematic order parameter values in every frame.
See also
References
 1
Allen, M. P.; Tildesley , D. J. (1987), “Computer Simulation of Liquids”, Ch. 11.5
 2
 3
Examples
Ordering of chains in an alkylsilane monolayer of C10H31Si(OH)2:
>>> import mdtraj as md >>> from mdtraj.testing import get_fn >>> traj = md.load(get_fn('monolayer.xtc'), top=get_fn('monolayer.pdb')) >>> # Each of the 100 chains contains 36 atoms. >>> chain_indices = [[n+x for x in range(36)] for n in range(0, 3600, 36)] >>> S2 = md.compute_nematic_order(traj, indices=chain_indices)
The chains were attached to a flat, crystalline substrate and are thus highly ordered with a mean S2 of ~0.996.
>>> traj = md.load(get_fn('tip3p_300K_1ATM.xtc'), top=get_fn('tip3p_300K_1ATM.pdb')) >>> water_indices = [[n+x for x in range(3)] for n in range(0, 3600, 3)] >>> S2 = md.compute_nematic_order(traj, indices=water_indices)
This water box is essentially isotropic and has a mean S2 of ~0.042.