treekin − Calculate a macrostate dynamics of biopolymers |
treekin [options] < foo.bar |
treekin computes a reduced dynamics of biopolymer
folding by means of a Markov process that (generally) operates at
the level of macrostates, i.e. basins of attraction in the underlying
energy landscapes. |
−a, −−absorb i |
Make a state i absorbing (default none) |
−m, −−method m |
Select method to build transition matrix. Possible values
for m are: |
−−p0 s=x |
Set the start population probability of state s to x. This option can be given multiple times. Note that the sum of all population probabilities must be 1. |
−−t0 time |
Set simulation start time in internal units (default 0.1) |
−−t8 time |
Set simulation stop time in internal units (default 1e+09) |
−−tinc increment |
Time scaling factor for logarithmic time scale (default 1.02) |
−T, −−Temp temp |
Set the simulation temperature in Celsius to temp (default 37.0) |
−−info |
Show all settings (default off) |
−h −−help |
Output help information and exit. |
−V −−version |
Output version information and exit. |
−b, −−bin |
read binary input (default= off) |
−d, −−degeneracy |
Consider degeracy in transition rates (default= off) |
−e, −−exponent |
Use matrix−expontent routines, NO diagonalization (default off) |
−−fpt |
calculate first passage times (default=off) |
−n, −−nstates num |
Read num states |
−r, −−recover |
Recover from pre−calculated Eigenvalues and Eigenvectors (default=off) |
−w −−wrecover |
Write recovery file containing Eigenvalues and Eigenvectors (default=off) |
−u, −−umatrix |
Dump transition matrix U to a binary file mx.bin (default= off) |
−x, −−mathematicamatrix |
Dump transition matrix U to Mathematica−readable file mxMat.txt (default=off) |
Typically, the first step is to compute an energy landscape by barriers: barriers −−saddle −−bsize −−rates < foo.sub > foo.bar the resulting barfile (foo.bar) and rates file (rates.out) are then processed by: treekin −−p0 2=1 −m I < foo.bar Here, the simulation starts with 100% of the initial
population in macrostate 2(second lowest local minimum in
the barrier tree). The transition matrix is constructed from
a set of microscopic rates (as computed by barriers).
Generally, the microstate dynamics is much more accurate
than the simple Arrhenius−like dynamics. |
If you use this program in your work you might want to cite: M.T. Wolfinger, W.A. Svrcek−Seiler, Ch. Flamm, I.L. Hofacker, P.F. Stadler (2004) Efficient Folding Dynamics of RNA Secondary Structures J.Phys.A: Math.Gen. 37: 4731−4741 I.L. Hofacker, Ch. Flamm, M.T. Wolfinger, P.F. Stadler (2004) Approximation of RNA Folding Kinetics Using Sequences of Barrier Trees. in preparation |
Michael Wolfinger, Ivo Hofacker, Christoph Flamm, Andreas Svrcek−Sailer, Peter Stadler. Send comments to <ivo@tbi.univie.ac.at> |
barriers(1) |