Relative path

../fullrmc/Examples/anglesConstraint/

Description

A water molecule is used to demonstrate how an angle constraint can be used to constraint bonded atoms angles. This example was used to generate the angle 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 water 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.

CREATE ENGINE:

Create the engine and the needed bonds and bond-angles 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 H-O-H bond angle to be between 80 and 120 degrees.
2. run_squeezed: Constraint H-O-H bond angle to be between 30 and 40 degrees.
3. run_streched: Constraint H-O-H bond angle to be between 160 and 170 degrees.

RUN SIMULATION:

Run in order all of ‘run_normal’, ‘run_squeezed’ and finally ‘run_streched’.

VISUALIZE SIMULATION:

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