Module: maze

Description	Usage
enhanced sampling methods for studying ligand unbinding from protein tunnels
Authors: Jakub Rydzewski

Details

maze is a module for PLUMED2, which implements enhanced sampling methods for ligand unbinding from protein tunnels. The maze module is developed and maintained by Jakub Rydzewski at the Institute of Physics, Nicolaus Copernicus University, Torun, Poland. See this link for additional information.

The maze module is an optional module for PLUMED2 that needs to be enabled when configuring the compilation of PLUMED2. You can either pass a flag --enable-modules=maze or a --enable-modules=all when running the configure script.

Actions

The following actions are part of this module

Tags

MAZE_LOSS_FUNCTION MAZE_OPTIMIZER MAZE_BIAS

MAZE_LOSS_FUNCTION: loss function for the maze module MAZE_OPTIMIZER: optimizer for the maze module MAZE_BIAS: bias for the maze module

Name	Description	Tags
MAZE_LOSS	Define a coarse-grained loss function describing interactions in a	MAZE_LOSS_FUNCTION
MAZE_MEMETIC_SAMPLING	Calculates the biasing direction along which the ligand unbinds by	MAZE_OPTIMIZER
MAZE_OPTIMIZER_BIAS	Biases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER.	MAZE_BIAS
MAZE_RANDOM_ACCELERATION_MD	Performs random acceleration MD within the protein matrix.	MAZE_OPTIMIZER
MAZE_RANDOM_WALK	Fake optimizer that can be used for debugging.	MAZE_OPTIMIZER
MAZE_SIMULATED_ANNEALING	Calculates the biasing direction along which the ligand unbinds by minimizing	MAZE_OPTIMIZER
MAZE_STEERED_MD	Performs a linear unbinding along a predefined biasing direction that	MAZE_OPTIMIZER