Action: PCARMSD
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the PCA components for a number of provided eigenvectors and an average structure. |   |
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 |
|---|---|---|
| eig | scalar | the projections on each eigenvalue are stored on values labeled eig-1, eig-2, |
| residual | scalar | the distance of the present configuration from the configuration supplied as AVERAGE in terms of mean squared displacement after optimal alignment |
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:
- L. Sutto, M. D’Abramo, F. L. Gervasio, Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin. Journal of Chemical Theory and Computation. 6, 3640–3646 (2010)
- V. Spiwok, P. Lipovová, B. Králová, Metadynamics in Essential Coordinates: Free Energy Simulation of Conformational Changes. The Journal of Physical Chemistry B. 111, 3073–3076 (2007)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| AVERAGE | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| EIGENVECTORS | compulsory | none | a file in pdb format containing the reference structure and the atoms involved in the CV |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |
| SQUARED_ROOT | optional | false | This should be set if you want RMSD instead of mean squared displacement |