Relative path

../fullrmc/Examples/improperConstraint/

Description

A pentafluoroxenate molecule is used to demonstrate how an improper angle constraint can be used to force the planarity of a molecule. This example was used to generate the improper 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 pentafluoroxenate 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, bond-angles and improper-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 \(\vec{F4}\) defined between F4 and F2 atoms to be within -2 and 2 degrees off the plane defined by the three atoms (F2, F1, F3). The same constraint applies for \(\vec{F5}\) and \(\vec{Xe}\) vectors.
2. run_loosen_1: Constraint \(\vec{F4}\) defined between F4 and F2 atoms to be within -60 and 50 degrees off the plane defined by the three atoms (F2, F1, F3). The same constraint applies for \(\vec{F5}\) and \(\vec{Xe}\) vectors.
3. run_loosen_2: Constraint \(\vec{F4}\) defined between F4 and F2 atoms to be within 50 and 60 degrees off the plane defined by the three atoms (F2, F1, F3). The same constraint applies for \(\vec{F5}\) and \(\vec{Xe}\) vectors.

RUN SIMULATION:

Run in order all of ‘run_normal’, ‘run_loosen_1’, ‘run_loosen_2’ and finally ‘run_normal’ again.

VISUALIZE SIMULATION:

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