Shortcut: ADAPTIVE_PATH
| Module | mapping |
|---|---|
| Description | Usage |
| Compute path collective variables that adapt to the lowest free energy path connecting states A and B. |   |
| output value | type |
| the position along and from the adaptive path | scalar |
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 list of arguments you would like to use in your definition of the path |
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 |
|---|---|---|---|
| ARG | input | none | the list of arguments you would like to use in your definition of the path |
| REFERENCE | compulsory | none | a pdb file containing the set of reference configurations |
| TYPE | compulsory | OPTIMAL-FAST | the manner in which distances are calculated |
| FIXED | compulsory | none | the positions in the list of input frames of the two path nodes whose positions remain fixed during the path optimization |
| HALFLIFE | compulsory | -1 | the number of MD steps after which a previously measured path distance weighs only 50 percent in the average |
| UPDATE | compulsory | none | the frequency with which the path should be updated |
| TOLERANCE | compulsory | 1E-6 | the tolerance to use for the path updating algorithm that makes all frames equidistant |
| FMT | compulsory | %f | the format to use for output files |
| WSTRIDE | compulsory | none | frequency with which to write out the path |
| COEFFICIENTS | optional | not used | the coefficients of the displacements along each argument that should be used when calculating the euclidean distance |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| NOSPATH | optional | false | do not calculate the spath CV |
| NOZPATH | optional | false | do not calculate the zpath CV |
| GPATH | optional | false | calculate the trigonometric path |
| PROPERTY | optional | not used | read in path coordinates by finding option with this label in remark of pdb frames |
| WFILE | optional | not used | file on which to write out the path |