#sequence
RNA A 2656     UACGUAAGUA

# stages
firstStage 1
lastStage 1

#general simulation parameters
baseInteractionScaleFactor     200
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

# Want to make a GNRA? Try the following:
#baseInteraction A 2662 Hoogsteen  A 2659 SugarEdge Trans
#baseInteraction A 2660 HelicalStackingA3 A 2661 HelicalStackingA5 Cis
#baseInteraction A 2661 HelicalStackingA3 A 2662 HelicalStackingA5 Cis
#baseInteraction A 2662 HelicalStackingA3 A 2663 HelicalStackingA5 Cis


numReportingIntervals 10

setDefaultMDParameters