Relative path

../fullrmc/Examples/translations/

Description

Here a single molecule is used to demonstrate how to use certain translation move generators. This example was used to generate the translation video example as seen in the online documentation. When running this example several files will be generated where all moved are saved. If VMD. is installed, the trajectory of all moves will be automatically visualized.

Files

1. molecule.pdb: The single molecule structure
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 set the only molecule as a rigid body. This is done automatically because set_groups_as_molecules will only find one molecule.

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. along_axis_0: Used to translate the molecule along its principal axis
2. along_axis_1: Used to translate the molecule along its secondary axis
3. along_axis_2: Used to translate the molecule along its tertiary axis
4. random: Used to translate the molecule randomly

RUN SIMULATION:

All four functions are called consecutively.

VISUALIZE SIMULATION:

Reset initial pdb to engine instance. Visualize engine along with all saved four trajectories “bonds.xyz”, “angles.xyz”, “both.xyz”.