Shortcut: RMSD
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the RMSD with respect to a reference structure. |   |
| output value | type |
| the RMSD distance between the instaneous structure and the reference structure/s that were input | scalar/vector |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. 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 | Keyword | Description |
|---|---|---|---|
| disp | vector/matrix | DISPLACEMENT | the vector of displacements for the atoms |
| dist | scalar/vector | DISPLACEMENT | the RMSD distance the atoms have moved |
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 |
|---|---|---|---|
| REFERENCE | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| TYPE | compulsory | SIMPLE | the manner in which RMSD alignment is performed |
| NUMBER | compulsory | 0 | if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here |
| 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 |
| DISPLACEMENT | optional | false | Calculate the vector of displacements instead of the length of this vector |