Relative path

../fullrmc/Examples/dihedralConstraint/

Description

A butane molecule is used to demonstrate how an dihedral angle constraint can be used to force a dihedral angle between two intersecting planes. 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 butane 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 dihedral-angles constraints. Notice that in the bonds constraint definition huge bonds of 100 angstroms are defined. This is done on purpose to constraints minimum intra-molecular distances similar to VDW forces. In fullrmc, dihedral angles can be constrained by three different shells set between 0 and 360 deg. at the same time. In this example we can see the initial definition setting the first shell between [30 deg.,90 deg.] and the second shell between [150 deg.,210 deg.] and the third shell between [270 deg.,330 deg.]

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_first_shell: Set dihedral constraint to a single shell between [150 deg.,210 deg.]
2. run_second_shell: Set dihedral constraint to a single shell between [10 deg.,30 deg.]
3. run_third_shell: Set dihedral constraint to a single shell between [90 deg.,100 deg.]

RUN SIMULATION:

Run in order all of ‘run_first_shell’, ‘run_second_shell’, and finally ‘run_third_shell’.

VISUALIZE SIMULATION:

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