ksim - Kinetic Folding Program for Nucleic Acids -
Usage: ksim [OPTION] < FILE
Options:
EnergyModel
--dangle <0|1|2> set dangling end model to (non|normal|double)
--Temp <float> set simulation temperature to <float>
--TempFile <string> use temperature file <string>
--Par <string> use energy-parameter-file <string>
--dna use DNA energy parameters
Note: This will only work if you have the
dna parameter file for ViennaRNA, 'dna.txt'
accessible in the current directory or path.
--logML use linear multiloop-function not logarithmic
MoveSet
--noShift turn off shift-moves
--noLP forbit structures with isolated base-pairs
Simulation
--seed <int=int=int> set random seed to <int=int=int>
--time <float> set maxtime of simulation to <folat>
--num <int> set number of simulations to <int>
--start set start structure
--stop set stop structure(s)
--nostop toggles the use of stop structure(s) off
--minima toggles printing of minima (by descent)
--met use Metropolis rule not Kawasaki rule
--fpt stop stop structure(s) is reached
Output
--log <string> set basename of log-file to <string>
--err <string> set basename of error-log-file to <string>
--silent no output to stdout
--verbose more information to stdout
--lmin output only local minima to stdout
--cut <float> output structures with E <= <float> to stdout
Default Settings:
EnergyModel
--dangle = 2
--Temp = 37.00
--TempFile =
--Par = VRNA-1.4
--dna = off
--logML = logarithmic
MoveSet
--noShift = off
--noLP = off
Simulation
--seed = clock
--time = 500.0
--num = 1
--start = OpenChain
--stop = Mfe
--nostop = Using stop structures
--minima = Not printing nearest minima
--met = Kawasaki
--fpt = on
Output
--log = kinout
--silent = off
--verbose = off
--lmin = off
--cut = 20.00
Input File Format:
1st line sequence
2nd line start structure (if option --start is used)
following lines stop structures
if --nostop is used, only the sequence is necessary, though a start structure may be specified
Sample command line:
ksim --verbose --num 100 --time 500 --minima --dna --nostop --log switch < ./switch.in > switch.traj
Runs 100 trials with the dna energy model, using the input file switch.in, with no set stop structures and also printing the "nearest" local minima.
Log goes to switch.log (note that the .log is added automatically) and the actual trajectories generated (by the verbose switch) go to switch.traj