Action: PATHMSD
| Module | colvar |
|---|---|
| Description | Usage |
| This Colvar calculates path collective variables. |   |
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 |
|---|---|---|
| sss | scalar | the position on the path |
| zzz | scalar | the distance from the path |
Further details and examples
Text from manual goes here
References
More information about how this action can be used is available in the following articles:
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| LAMBDA | compulsory | none | the lambda parameter is needed for smoothing, is in the units of plumed |
| REFERENCE | compulsory | none | the pdb is needed to provide the various milestones |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| NEIGH_SIZE | optional | not used | size of the neighbor list |
| NEIGH_STRIDE | optional | not used | how often the neighbor list needs to be calculated in time units |
| EPSILON | optional | not used | the maximum distance between the close and the current structure, the positive value turn on the close structure method |
| LOG_CLOSE | optional | not used | value 1 enables logging regarding the close structure |
| DEBUG_CLOSE | optional | not used | value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower |