Action: MAZE_MEMETIC_SAMPLING

Module	maze
Description	Usage
Calculates the biasing direction along which the ligand unbinds by

Details and examples

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

MAZE_MEMETIC_SAMPLINGCalculates the biasing direction along which the ligand unbinds by More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=maThe MAZE_MEMETIC_SAMPLING action with label ma calculates the following quantities:
 Quantity   
 Type   
 Description  
ma.x
scalar
Optimal biasing direction; x component.
ma.y
scalar
Optimal biasing direction; y component.
ma.z
scalar
Optimal biasing direction; z component.
ma.loss
scalar
Loss function value defined by the provided pairing function.
ma.sr
scalar
Sampling radius. Reduces sampling to the local proximity of the ligand position.

  LOSSLoss function describing ligand-protein interactions required by every optimizer=l

  N_ITERNumber of optimization steps=10
  OPTIMIZER_STRIDEOptimizer stride=200

  CAPACITYSampling set size=20

  LOCAL_SEARCH_ON Turn local search on
  N_LOCAL_ITERNumber of local search iterations=10
  LOCAL_SEARCH_RATERate of mutation in local search=0.1
  LOCAL_SEARCH_TYPEType of local search=stochastic_hill_climbing

  MUTATION_RATEProbability of mutation=0.1
  MATING_RATEProbability of mating=0.7
  CAUCHY_ALPHAMean of Cauchy distribution for sampling=0
  CAUCHY_BETASpread of Cauchy distribution for sampling=0.1

  LIGANDIndices of ligand atoms=2635-2646
  PROTEINIndices of protein atoms=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.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
LIGAND	atoms	Indices of ligand atoms
PROTEIN	atoms	Indices of protein atoms

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Description
x	scalar	Optimal biasing direction; x component
y	scalar	Optimal biasing direction; y component
z	scalar	Optimal biasing direction; z component
loss	scalar	Loss function value defined by the provided pairing function
sr	scalar	Sampling radius

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
LIGAND	input	none	Indices of ligand atoms
PROTEIN	input	none	Indices of protein atoms
N_ITER	compulsory	none	Number of optimization steps
OPTIMIZER_STRIDE	compulsory	none	Optimizer stride
CAPACITY	compulsory	none	Sampling set size
MUTATION_RATE	compulsory	none	Probability of mutation
MATING_RATE	compulsory	none	Probability of mating
CAUCHY_ALPHA	compulsory	none	Mean of Cauchy distribution for sampling
CAUCHY_BETA	compulsory	none	Spread of Cauchy distribution for sampling
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
SERIALThis keyword do not have examples	optional	false	Perform the simulation in serial -- used only for debugging purposes, should not be used otherwise
PAIRThis keyword do not have examples	optional	false	Pair only the 1st element of the 1st group with the 1st element in the second, etc
NLISTThis keyword do not have examples	optional	false	Use a neighbor list of ligand-protein atom pairs to speed up the calculating of the distances
NL_CUTOFFThis keyword do not have examples	optional	not used	Neighbor list cut-off for the distances of ligand-protein atom pairs
NL_STRIDEThis keyword do not have examples	optional	not used	Update stride for the ligand-protein atom pairs in the neighbor list
LOSS	optional	not used	Loss function describing ligand-protein interactions required by every optimizer
LOCAL_SEARCH_ON	optional	false	Turn local search on
N_LOCAL_ITER	optional	not used	Number of local search iterations
LOCAL_SEARCH_RATE	optional	not used	Rate of mutation in local search
LOCAL_SEARCH_TYPE	optional	not used	Type of local search