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Folding Modes:
(1) default mode:
start structure is open chain
stop structure is minimum free enegy structure
example: hairpin.log, traj
../Kinfold --log hpin --num 10 <./hpin.in>& traj
(2) multi-stop mode:
start structure is open chain
stop structure(s) are 2nd and following lines in hpin.in
example: hairpin.e.log, traj.e
../Kinfold --stop --log hpin.e --num 10 <./hpin.in>& traj.e
(3) refolding mode:
start structure is 2nd line in hpin.in
stop structure(s) are 3rd and following lines in hpin.in
example: hairpin.ae.log, traj.ae
../Kinfold --start --stop --log hpin.ae --num 10 <./hpin.in>& traj.ae
if you don't want to log the trajectories use option --silent
(trajectory files can get petty huge)
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Output:
(A) log files (on each line you find):
randon seed
stop-structure-label or O ( for didn't reach stop-structure(s) )
first passage time
stop-structure if stop-structure-label equals O
(B) trajectory files (on each line you find):
structure
energy
time
number of neighbours of structure (only with --verbose)
code for the move (only with --verbose)
(i=base pair insert move,
d=base pair delete move,
s,S=base pair shift move,
I=base pair double insert move (only with --noLP)
D=base pair double delete move (only with --noLP)
)
code for type of structure (only with --verbose)
(1=strict local minimum,
2=degenerate local minimum,
0=anything else
)
stop-structure-label or O ( for didn't reach stop-structure(s) )
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canonical example: hpin.nolp, traj.nolp
../Kinfold --verbose --noLP --num 10 --log hpin.nolp < ./hpin.in > traj.nolp