Skip to content

Compute folding dynamics on coarse grained version of an energy landscape by numeric integration of a Markov process

License

Notifications You must be signed in to change notification settings

ViennaRNA/Treekin

Repository files navigation

GitHub release Build Status Github All Releases Conda AUR

Treekin

Compute folding dynamics on coarse grained energy landscapes through numeric integration of the underlying Markov process


Description

The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100-1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix).

For detailed instructions see the man page.


ATTENTION:

use --rrecover and --wrecover options with caution:

first: run treekin with -w, i.e. let it diagonalize the input matrix once and write the eigenvalues and eigenvectors to the corresponding *.{evals,evecs}.bin files

second: run treekin with the -r option, i.e let it read those *.{evals,evecs}.bin files and do ONLY the iteration (no diagonalization)

NOTE: when using --rrecover and --wrecover option in combination with the -a option, treekin assumes that the absorbing state between consecutive calls of the program are the same (since the information about the absorbing state influences the transition matrix). If you change the -a option while calling treekin with --rrecover, treekin will produce junk output (since the transition matrix that has been diagonalized earlier is different from the current one, due to the different absorbing state)


References

If you use this software, you may want to cite the follwing publications:


License

Please read the copyright notice in the file COPYING!

If you want to include this software in a commercial product, please contact the authors.

About

Compute folding dynamics on coarse grained version of an energy landscape by numeric integration of a Markov process

Resources

License

Stars

Watchers

Forks

Packages

No packages published