The program for finding the optimal path in complex free energy landscape (for example oxygen pathways in protein).
- A starting point for wavefront (e.g. an active site of a protein) is chosen and Eikonal equation is solved using finite-differences method. This procedure calculates 3D map of wavefront arrival times.
- Area where wavefont exits the protein is located and used as a starting point for gradient descent algorithm to find the optimal path back to the source of the wave.
- The cost of the path and the free energy profile is computed by projecting the free energy map on the path.
- 3D slowness map of the media in DX format.
- User configurable parameters: "eikonal.in".
Run the executable "eikonal" from the folder with the configuration file "eikonal.in"
- Wavefront arrival times: times.dx
- The optimal path: path.xyz
- Free energy profile along the path: pmf.dat
- T. Zaraiskaya, S. Vassiliev, D. Bruce, Discovering oxygen channel topology in photosystem II using implicit ligand sampling and wavefront propagation, J. Comput. Sci. 5 (2014) 549–555. doi:10.1016/j.jocs.2013.10.001.
- S. Vassiliev, T. Zaraiskaya, D. Bruce, Molecular dynamics simulations reveal highly permeable oxygen exit channels shared with water uptake channels in photosystem II, Biochim. Biophys. Acta BBA - Bioenerg. 1827 (2013) 1148–1155. doi:10.1016/j.bbabio.2013.06.008.