#sequence
RNA A 2656 UACGUAAGGA

# stages
firstStage 1
lastStage 2

#general simulation parameters
baseInteractionScaleFactor     20
reportingInterval 4.0
temperature 10 
randomizeInitialVelocities TRUE

#base pairing forces to generate the hairpin 
baseInteraction A 2658 WatsonCrick A 2663 WatsonCrick Cis 
baseInteraction A 2657 WatsonCrick  A 2664 WatsonCrick Cis 
baseInteraction A 2656 WatsonCrick  A 2665 WatsonCrick Cis

# During stage 1, quickly form helix by ignoring steric clashes.  Clashes and tangles may occur here, but we’ll deal with them next..
readAtStage 1
numReportingIntervals 10
readBlockEnd


# During stage 2, do a de-tangling and de-clashing run.
# Remember, there is a stochastic element .. you may need to run this more than once to get convergence.
readAtStage 2
# All forces (including base pairing and collision-detecting sphere forces) are inactive for scrubberPeriod*(dutyCycle-1) picoseconds, and active for scrubberPeriod*dutyCycle picoseconds.  Note that dutyCycle defaults to 1.0:
dutyCycle .9 
scrubberPeriod 40
# add collision-detecting steric spheres to all atoms except hydrogen.  Note that the radius and stiffness of these spheres is set with the excludedVolumeRadius and excludedVolumeStiffness parameters:
contact AllHeavyAtomSterics A
readBlockEnd



#some hints for the GNRA tetraloop:
#baseInteraction A xxxx Hoogsteen  A xxxx SugarEdge Trans  
#baseInteraction A xxxx Stacking A xxxx Stacking Cis