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 random acceleration MD within the protein matrix.

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.
dist Distance traveled in one sampling interval.
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.
R_MIN Minimal distance traveled before sampling a new direction of biasing.
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.

( 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.

Every optimizer implemented in the maze module needs a loss function as an argument, and it should be passed using the MAZE_LOSS keyword.




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