MAZE_SIMULATED_ANNEALING

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 simulated annealing.

- 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.

In the following example simulated annealing is launched for 1000 iterations as the optimizer for the loss function every 200 ps. The geometric cooling scheme is used.

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

UNITSLENGTH=Athe units of lengths.TIME=psthe units of time.ENERGY=kcal/molthe units of energy.sa:MAZE_SIMULATED_ANNEALING ...LOSS=lLoss function describing ligand-protein interactions required by every optimizer.N_ITER=1000compulsory keywordNumber of optimization steps.OPTIMIZER_STRIDE=200compulsory keywordOptimizer stride.PROBABILITY_DECREASER=300compulsory keywordTemperature-like parameter that is decreased during optimization to modify the Metropolis-Hastings acceptance probability.COOLING=0.95compulsory keywordReduction factor for PROBABILITY_DECREASER, should be in (0, 1].COOLING_TYPE=geometriccould not find this keywordLIGAND=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.

- 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. |

PROBABILITY_DECREASER | Temperature-like parameter that is decreased during optimization to modify the Metropolis-Hastings acceptance probability. |

COOLING | Reduction factor for PROBABILITY_DECREASER, should be in (0, 1]. |

COOLING_SCHEME | Cooling scheme: geometric. |

- 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. |

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. |