Relative path

../fullrmc/Examples/coordNumConstraint/

Description

A created AlCl2F2 is created to demonstrate how atomic coordination number constraint works and can be used to force atoms coordination. This example was used to generate the coordination number constraint video example as seen in the online documentation. When running this example a trajectory file will be generated. If VMD. is installed, the trajectory of all moves will be automatically visualized.

Files

1. system.pdb: The AlCl2F2 molecule pdb file
2. run.py: The script file used to run the simulation

run.py explained

IMPORTING USEFUL DEFINITIONS:

All useful packages, modules and definitions are imported.

SHUT DOWN LOGGING:

Set logger minimum level to maximum possible integer value. This will mute all non-error logging.

XY TRANSLATION GENERATOR:

Defining XYTranslationGenerator move generator class. This move generator is used to move groups randomly in only XY plane. Defining a move generator is as easy as overloading the method ‘transform_coordinates’ which is used by the engine to move atoms’ coordinates.

CREATE ENGINE:

Create the engine as well as the needed Inter-molecular distance and atomic coordination number constraints.

DIFFERENT RUNS:

Define functions to run fitting engine. All of the following functions finish running the engine using Engine.run method. A trajectory of all moves is saved to the disk by setting XYZPath argument not to None.

1. run_normal: Constraint both chlorine atoms to be within aluminum coordination shell between 1.5 and 2.5 \(\AA\). Same way constraint both sulfur atom to be in a coordination shell between 2.5 and 3 \(\AA\).

RUN SIMULATION:

Run ‘run_normal’ and generate a 10000 steps trajectory

VISUALIZE SIMULATION:

Reset initial pdb to engine instance. Visualize engine along with the saved trajectory “trajectory.xyz”.