#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