Action: FUNNEL_PS
| Module | funnel |
|---|---|
| Description | Usage |
| FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. |   |
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 |
|---|---|---|
| lp | scalar | the position along the funnel line |
| ld | scalar | the distance from the funnel line |
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 | This MUST be a single atom, normally the COM of the ligand |
| ANCHOR | atoms | Closest protein atom to the ligand, picked to avoid pbc problems during the simulation |
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 | This MUST be a single atom, normally the COM of the ligand |
| ANCHOR | input | none | Closest protein atom to the ligand, picked to avoid pbc problems during the simulation |
| REFERENCE | compulsory | none | a file in pdb format containing the structure you would like to align |
| POINTS | compulsory | none | 6 values defining x, y, and z of the 2 points used to construct the line |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| SQUARED-ROOT | optional | false | Used to initialize the creation of the alignment variable |