MAZE_STEERED_MD

	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.

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

smd: MAZE_STEERED_MD ...
   
   
LOSS
Loss function describing ligand-protein interactions required by every optimizer.
=l 
   
PULLING
compulsory keyword 
Constant biasing direction. 
=0.3,0.3,0.3 
   
OPTIMIZER_STRIDE
compulsory keyword 
Optimizer stride. 
=_ 
   
LIGAND
Indices of ligand atoms.. 
=2635-2646 
   
PROTEIN
Indices of protein atoms.. 
=1-2634 
... You cannot view the components that are calculated by each action for this input file. Sorry 

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.
tdist	Total distance traveled by biased atoms.

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

OPTIMIZER_STRIDE	Optimizer stride. Sets up a callback function that launches the optimization process every OPTIMIZER_STRIDE.
PULLING	Constant biasing direction.

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=off ) 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.