# 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.

References

1

Allen, M. P.; Tildesley , D. J. (1987), “Computer Simulation of Liquids”, Ch. 11.5

2

http://cmt.dur.ac.uk/sjc/thesis_dlc/node65.html

3

http://cmt.dur.ac.uk/sjc/thesis_dlc/node19.html

Examples

Ordering of chains in an alkylsilane monolayer of C10H31-Si(OH)2-:

>>> import mdtraj as md
>>> from mdtraj.testing import get_fn

>>> traj = md.load(get_fn('tip3p_300K_1ATM.xtc'), top=get_fn('tip3p_300K_1ATM.pdb'))