Shortcut: DRMSD
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the distance RMSD with respect to a reference structure. |   |
| output value | type |
| the DRMSD distance between the instantaneous structure and the reference structure | scalar/vector |
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 |
|---|---|---|---|
| REFERENCE | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| TYPE | compulsory | DRMSD | what kind of DRMSD would you like to calculate |
| LOWER_CUTOFF | optional | not used | only pairs of atoms further than LOWER_CUTOFF are considered in the calculation |
| UPPER_CUTOFF | optional | not used | only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation |
| SQUARED | optional | false | This should be setted if you want MSD instead of RMSD |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |