Action: MAZE_OPTIMIZER_BIAS

Module	maze
Description	Usage
Biases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER.

Details and examples

Biases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER.

OptimizerBias is a class deriving from Bias, and it is used to adaptively bias a ligand-protein system toward an optimal solution found by the chosen MAZE_OPTIMIZER (see the module page and select MAZE_OPTIMIZER from the tags dropdown for the list of permitted optimizers).

Remember to define the loss function (MAZE_LOSS) and the optimizer prior to the adaptive bias for the optimizer.

The adaptive bias potential is the following:

$$V({\bf x}_t)=\alpha \left(wt - ({\bf x} - {\bf x}^*_{t-\tau}) \cdot \frac{{\bf x}^*_t - {\bf x}_t}{\|{\bf x}^*_t-{\bf x}_t\|} \right)^2,$$

where ${\bf x}^*_t$ is the optimal solution at time $t$, $w$ is the biasing rate, $\tau$ is the interval at which the loss function is minimized, and $\alpha$ is a scaled force constant.

Examples

In the following example the bias potential biases a ligand atom (which have to be given as an argument) with the biasing rate equal to 0.02 A/ps, and the biasing constant equal to 3.6 kcal/(mol A). It also takes an optimizer (see the module page and select MAZE_OPTIMIZER from the tags dropdown for the list of permitted optimizers).

Click on the labels of the actions for more information on what each action computes

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingp: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=2635 NOPBC ignore the periodic boundary conditions when calculating distances

The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positionMAZE_OPTIMIZER_BIASBiases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=bias

  ARGthe labels of the scalars on which the bias will act=p.x,p.y,p.z

  BIASING_RATEBiasing rate=0.02
  ALPHARescaled force constant=3.6

  OPTIMIZEROptimization technique to minimize the collective variable for ligand     unbinding: RANDOM_WALK,                STEERED_MD,                RANDOM_ACCELERATION_MD,                SIMULATED_ANNEALING,                MEMETIC_SAMPLING=opt
... MAZE_OPTIMIZER_BIAS
The MAZE_OPTIMIZER_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.bias
the instantaneous value of the bias potential
bias.force2
Square of the biasing force
bias.x
Optimal biasing direction: x component
bias.y
Optimal biasing direction: y component
bias.z
Optimal biasing direction: z component
bias.tdist
Total distance traveled by biased atoms

Input

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

Keyword	Type	Description
ARG	scalar	the labels of the scalars on which the bias will act

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
bias	scalar	the instantaneous value of the bias potential
force2	scalar	Square of the biasing force
x	scalar	Optimal biasing direction: x component
y	scalar	Optimal biasing direction: y component
z	scalar	Optimal biasing direction: z component
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
ARG	input	none	the labels of the scalars on which the bias will act
BIASING_RATE	compulsory	none	Biasing rate
ALPHA	compulsory	none	Rescaled force constant
OPTIMIZER	compulsory	none	Optimization technique to minimize the collective variable for ligand unbinding: RANDOM_WALK, STEERED_MD, RANDOM_ACCELERATION_MD, SIMULATED_ANNEALING, MEMETIC_SAMPLING
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically