Module: mapping
| Description | Usage |
|---|---|
| actions for definining linear and curvilinear paths and manifolds in a higher dimensional space | |
| Authors: Gareth Tribello |   |
Details
The tools in this module are used to define a subspace in some higher dimensional space. As discussed in the papers cited below this subspace can be a defined using a set of linear projections from the high dimensional space to some lower dimensional linear space or it can be a curilinear path or curvilinear manifold. Furthermore, the high dimensional space can describe the positions of all or a subset of the atoms in your system or it can be defined using a large number of collective variables.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| ADAPTIVE_PATH | Compute path collective variables that adapt to the lowest free energy path connecting states A and B. | COLVAR |
| AVERAGE_PATH_DISPLACEMENT | Accumulate the distances between the reference frames in the paths and the configurations visited | ANALYSIS |
| GEOMETRIC_PATH | Distance along and from a path calculated using geometric formulas | COLVAR |
| GPATH | Distance along and from a path calculated using geometric formulas | COLVAR |
| GPROPERTYMAP | Property maps but with a more flexible framework for the distance metric being used. | COLVAR |
| PATH | Path collective variables with a more flexible framework for the distance metric being used. | COLVAR |
| PCAVARS | Projection on principal component eigenvectors or other high dimensional linear subspace | COLVAR |
| REPARAMETERIZE_PATH | Take an input path with frames that are not equally spaced and make the frames equally spaced | ANALYSIS |
Command line tools
The following command line tools are part of this module
| Name | Description |
|---|---|
| pathtools | print out a description of the keywords for an action in html |
References
More information about this module 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)
- D. Branduardi, F. L. Gervasio, M. Parrinello, From A to B in free energy space. The Journal of Chemical Physics. 126 (2007)
- M. Bonomi, D. Branduardi, F. L. Gervasio, M. Parrinello, The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin. Journal of the American Chemical Society. 130, 13938–13944 (2008)
- V. Spiwok, B. Králová, Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. The Journal of Chemical Physics. 135 (2011)
- G. Díaz Leines, B. Ensing, Path Finding on High-Dimensional Free Energy Landscapes. Physical Review Letters. 109 (2012)