Action: MAZE_STEERED_MD

Module	maze
Description	Usage
Performs a linear unbinding along a predefined biasing direction that

Details and examples

Performs a linear unbinding along a predefined biasing direction that needs to be provided using the PULLING keyword.

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_STEERED_MDPerforms a linear unbinding along a predefined biasing direction that More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=smd

  LOSSLoss function describing ligand-protein interactions required by every optimizer=l
  PULLINGConstant biasing direction=0.3,0.3,0.3
  OPTIMIZER_STRIDEOptimizer stride=_

  LIGANDIndices of ligand atoms=2635-2646
  PROTEINIndices of protein atoms=1-2634
... MAZE_STEERED_MD
The MAZE_STEERED_MD action with label smd calculates the following quantities:
 Quantity   
 Description  
smd.x
Optimal biasing direction; x component
smd.y
Optimal biasing direction; y component
smd.z
Optimal biasing direction; z component
smd.loss
Loss function value defined by the provided pairing function
smd.sr
Sampling radius
smd.tdist
Total distance traveled by biased atoms

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

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
tdist	scalar	Total distance traveled by biased atoms

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
OPTIMIZER_STRIDE	compulsory	none	Optimizer stride
PULLING	compulsory	none	Constant biasing direction
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