Compute folding dynamics on coarse grained version of an energy landscape
C C++ Roff M4 Other
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packaging
AUTHORS
COPYING
ChangeLog
INSTALL
Makefile.am
NEWS
README
autogen.sh
barparser.c
barparser.h
calc.c
calc.h
calcpp.cpp
calcpp.h
configure.ac
exp_matrix.c
exp_matrix.h
globals.c
globals.h
main.c
matrix.h
mxccm.c
mxccm.h
treekin.1
treekin.ggo

README

ATTENTION:
use --rrecover and --wrecover options with catution:
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)