5 Minutes Tutorial

System

  1. Obtain the trajectory from the molecular dynamics production run.

Note

Example system : 550 TIP3P water molecules with box length of 25.5 Å * 25.5 Å * 25.5 Å

alternate text

2. Generate the xyz file (input for the order package) from the trajectory with the atoms (O or center of mass) necessary to calculate the local structure.

Note

This xyz file should include all the water Oxygen atoms and all the other atoms that are cosidered as the closest neighbors. Make sure to follow the following file format for the xyz file. In this example the central Oxygen atoms of water are named as “OW”.

Line #1 : Number of atoms

Line #2 : BoxlenghtX(Space)BoxlenghtY(Space)BoxlenghtZ

Line #3 & onwards : Symbol assigned by the user for the central atom and the other atoms that can be considered as the closest neighbors

alternate text

3. Commands available in the package

$order [input] [-h] [-t TASK] [-c CENTER] [-b BINS] [-f FREQUENCY] [-p PLOT]

input

File name of the xyz file

-h

Show this help message and exit

-t TASK

Specification of the type of task that you need to perform. TASK can
be oto or tto or avc (default: oto).
If you need to perform multiple tasks simultaneously use a "," to
separate the tasks. (Ex : tto,oto)

-c CENTER

Type of center atom (default: 'O')
(In the example mentioned above the center is 'OW')

-b BINS

Number of bins for the parameter (default: 100)

-f FREQUENCY

Compute the parameter every n frame(s) in the xyz file(default: 1)

-p PLOT

Turn on / off of plotting (default: on)

Orientational Tetrahedral Order (OTO)

This is the most common type of tetrahedral ordr paramater that is being used. This order parameter uses the four closest water Oxygen neighbors for the calculation. The value of q can rang from 0 to 1, where 0 is for an ideal gas and 1 is for a regular tetrahedron.

\[q = 1 - \frac{3}{8}\sum_{j=1}^{3}\sum_{k=j+1}^{4}\left ( \cos \psi _{jk}+\frac{1}{3} \right )^{2}\]

q = Orientational tetrahedral order parameter

ψjk = Angle formed by the Oxygen atom under consideration & the two nearest neighbor atoms j & k

$order test.xyz -t oto -c 'OW' -f 5
alternate text

Translational Tetrahedral Order (TTO)

Similar to orientational tetrahedral order. But here, the variance of the radial distnace between the central water Oxygen atom and the four nearest neighbors are calculated. THe value of Skis close to 1 and quals 1 for the perfect tetrahedron. As the local tetrahedral nature increases, Skbecomes more closer to 1.

\[S_{k} = 1 - \frac{1}{3}\sum_{k=1}^{4}\frac{(r_{k} - \bar{r})^2}{4\bar{r}^2}\]

Sk = Translational tetrahedral order parameter

rk = Radial distance from the cental Oxygen atom to the k th peripheral closest neighbor

\(\bar{r}\) = Arithmatic mean of the four radial distances

$order test.xyz -t tto -c 'OW' -f 5

You can get the average Skvalue for your system by getting the average value of the raw_data output file.

Average value for Skfor the example is 0.998892128

Asphericity of the Voronoi Cell (AVC)

Asphericity parameter (\(\eta\)) can be used to characterize the shape of the Voronoi polyhedron. This value is independent of the size of the polyhedron. The value of \(\eta\) for a perfect sphere the is 1, for ice is 2.25 and for a regular tetrahedron it is 3.31. [Duboué-Dijon2015]

\[\eta = \frac{A^3}{36\pi V^2}\]

\(\eta\) = Asphericity parameter

A = Area of the polyhedron

V = Volume of the polyhedron

$order test.xyz -t avc -c 'OW' -f 5
alternate text
[Duboué-Dijon2015]DOI: 10.1021/acs.jpcb.5b02936