Action: PINES
| Module | pines |
|---|---|
| Description | Usage |
  |
Details and examples
//Documentation to be added.
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| SWITCHThis keyword do not have examples | compulsory | none | The switching functions parameter |
| REF_FILEThis keyword do not have examples | compulsory | none | PDB file name that contains the information about system connectivity and labels |
| N_BLOCKSThis keyword do not have examples | compulsory | none | Number of blocks in PIV |
| BUFFERThis keyword do not have examples | compulsory | none | Number of additional pairwise distances to include as a buffer for each PIV block |
| PL_REFRESHThis keyword do not have examples | compulsory | none | Upper limit refresh rate for each block pair list |
| SIZEThis keyword do not have examples | compulsory | none | Length of each PIV Block |
| NUMERICAL_DERIVATIVESThis keyword do not have examples | optional | false | calculate the derivatives for these quantities numerically |
| NOPBCThis keyword do not have examples | optional | false | ignore the periodic boundary conditions when calculating distances |
| BLOCKThis keyword do not have examples | optional | not used | Each block of the PIV |
| ATOMIDThis keyword do not have examples | optional | not used | AtomIDs |
| RESIDThis keyword do not have examples | optional | not used | ResIDs |
| NAMEThis keyword do not have examples | optional | not used | Atom Names |
| EXCLUDE_PAIRSThis keyword do not have examples | optional | not used | Excluded pairs |
| DRIVERMODEThis keyword do not have examples | optional | false | Use when post-processing a trajectory |
| FREEZE_SELECTIONThis keyword do not have examples | optional | false | Freeze top-K membership during derivative checks |