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.

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=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.
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.

MAZE_STEERED_MD ...
LABEL=smd

LOSS=l
PULLING=0.3,0.3,0.3
OPTIMIZER_STRIDE=_

LIGAND=2635-2646
PROTEIN=1-2634
... MAZE_STEERED_MD


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