Action: MAZE_STEERED_MD
| Module | maze |
|---|---|
| Description | Usage |
| Performs a linear unbinding along a predefined biasing direction that |   |
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 |
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 |
Further details and examples
Text from manual goes here
Syntax
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_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| SERIAL | optional | false | Perform the simulation in serial – used only for debugging purposes, should not be used otherwise |
| PAIR | optional | false | Pair only the 1st element of the 1st group with the 1st element in the second, etc |
| NLIST | optional | false | Use a neighbor list of ligand-protein atom pairs to speed up the calculating of the distances |
| NL_CUTOFF | optional | not used | Neighbor list cut-off for the distances of ligand-protein atom pairs |
| NL_STRIDE | 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 |