Compute folding dynamics on coarse grained energy landscapes through numeric integration of the underlying Markov process
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.
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)
If you use this software, you may want to cite the follwing publications:
- M.T. Wolfinger et al., "Efficient computation of RNA folding dynamics", J. Phys. A: Math. Gen. 37 4731
Please read the copyright notice in the file COPYING!
If you want to include this software in a commercial product, please contact the authors.