Relative path

../fullrmc/Examples/refine/

Description

A box of water molecules is used to demonstrate how to use fitting explore mode. This example was used to generate the refine video example as seen in the online documentation. When running this example a trajectory file will be generated where all moved are saved. If VMD. is installed, the trajectory of all moves will be automatically visualized.

Files

1. system.pdb: The initial configuration input 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.

BIASED ENGINE DEFINTION:

fullrmc Engine class is overloaded. This is an advanced new engine run method definition. It’s defined especially for this example. It must not be used in any other real scientific fitting.

CREATE ENGINE:

Create the engine and the needed inter-molecular distance constraint.

DIFFERENT RUNS:

Define refine to run the fitting engine. This function finishs 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. explore: Groups are using engine set_groups_as_molecules method. Then only first group is kept in the engine keeping all water molecules fixed. A collection MoveGeneratorCollector of move generators is created and set to the remaining group. RotationGenerator and TranslationGenerator are added to this collection. In order to perform any none traditional fitting mode, RecursiveGroupSelector must be used. In this case RandomSelector is passed to the recursive selector with refine flag set to True.

RUN SIMULATION:

refine function is called.

VISUALIZE SIMULATION:

Reset initial pdb to engine instance. Visualize engine along with otherParams argument set to [‘mol new trajectory.xyz’, ‘mol modstyle 0 1 VDW’] because only the exploring trajectory is saved and it needs to be loaded as new mol in VMD.