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.

- 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.

Click on the labels of the actions for more information on what each action computes

ma:MAZE_MEMETIC_SAMPLING ...LOSS=lLoss function describing ligand-protein interactions required by every optimizer.N_ITER=10compulsory keywordNumber of optimization steps.OPTIMIZER_STRIDE=200compulsory keywordOptimizer stride.CAPACITY=20compulsory keywordSampling set size.LOCAL_SEARCH_ON( default=off ) Turn local search on.N_LOCAL_ITER=10Number of local search iterations.LOCAL_SEARCH_RATE=0.1Rate of mutation in local search.LOCAL_SEARCH_TYPE=stochastic_hill_climbingType of local search.MUTATION_RATE=0.1compulsory keywordProbability of mutation.MATING_RATE=0.7compulsory keywordProbability of mating.CAUCHY_ALPHA=0compulsory keywordMean of Cauchy distribution for sampling.CAUCHY_BETA=0.1compulsory keywordSpread of Cauchy distribution for sampling.LIGAND=2635-2646Indices of ligand atoms..PROTEIN=1-2634 ...Indices of protein atoms..

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.

- Glossary of keywords and components

- 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. |