MAZE_MEMETIC_SAMPLING

This is part of the maze module | |

It is only available if you configure PLUMED with ./configure –enable-modules=maze . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |

Calculates the biasing direction along which the ligand unbinds by minimizing the MAZE_LOSS function. The optimal biasing direction is determined by performing a population-based memetics search with local heuristics.

- Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity | Description |

x | Optimal biasing direction; x component. |

y | Optimal biasing direction; y component. |

z | Optimal biasing direction; z component. |

loss | Loss function value defined by the provided pairing function. |

sr | Sampling radius. Reduces sampling to the local proximity of the ligand position. |

- The atoms involved can be specified using

LIGAND | Indices of ligand atoms.. For more information on how to specify lists of atoms see Groups and Virtual Atoms |

PROTEIN | Indices of protein atoms.. For more information on how to specify lists of atoms see Groups and Virtual Atoms |

- Compulsory keywords

N_ITER | Number of optimization steps. Required only for optimizers, do not pass this keyword to the fake optimizers (results in crash) , e.g., random walk, steered MD, or random acceleration MD. |

OPTIMIZER_STRIDE | Optimizer stride. Sets up a callback function that launches the optimization process every OPTIMIZER_STRIDE. |

CAPACITY | Sampling set size. |

MUTATION_RATE | Probability of mutation. |

MATING_RATE | Probability of mating. |

CAUCHY_ALPHA | Mean of Cauchy distribution for sampling. |

CAUCHY_BETA | Spread of Cauchy distribution for sampling. |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

SERIAL | ( default=off ) Perform the simulation in serial – used only for debugging purposes, should not be used otherwise. |

PAIR | ( default=off ) Pair only the 1st element of the 1st group with the 1st element in the second, etc. |

NLIST | ( default=on ) Use a neighbor list of ligand-protein atom pairs to speed up the calculating of the distances. |

LOCAL_SEARCH_ON | ( default=off ) Turn local search on. |

NL_CUTOFF | Neighbor list cut-off for the distances of ligand-protein atom pairs. |

NL_STRIDE | Update stride for the ligand-protein atom pairs in the neighbor list. |

LOSS | Loss function describing ligand-protein interactions required by every optimizer. |

N_LOCAL_ITER | Number of local search iterations. |

LOCAL_SEARCH_RATE | Rate of mutation in local search. |

LOCAL_SEARCH_TYPE | Type of local search. |

- Examples

Every optimizer implemented in the maze module needs a loss function as an argument, and it should be passed using the MAZE_LOSS keyword.

MAZE_MEMETIC_SAMPLING ... LABEL=ma LOSS=l N_ITER=10 OPTIMIZER_STRIDE=200 CAPACITY=20 LOCAL_SEARCH_ON N_LOCAL_ITER=10 LOCAL_SEARCH_RATE=0.1 LOCAL_SEARCH_TYPE=stochastic_hill_climbing MUTATION_RATE=0.1 MATING_RATE=0.7 CAUCHY_ALPHA=0 CAUCHY_BETA=0.1 LIGAND=2635-2646 PROTEIN=1-2634 ... MAZE_MEMETIC_SAMPLING

As shown above, each optimizer should be provided with the LIGAND and the PROTEIN keywords.

The neighbor list can be turned on by providing the NLIST keyword.