#sequence
RNA A 2656 UACGUAAGGA

#run parameters
reportingInterval 4
numReportingIntervals  40
firstStage 1
lastStage 1

randomizeInitialVelocities true

#general simulation parameters
baseInteractionScaleFactor     20
addAllHeavyAtomSterics  True
temperature 100.0 


#base pairing forces
baseInteraction A 2658 WatsonCrick A 2663 WatsonCrick Cis 
baseInteraction A 2657 WatsonCrick  A 2664 WatsonCrick Cis 
baseInteraction A 2656 WatsonCrick  A 2665 WatsonCrick Cis

#some hints for the GNRA tetraloop:
#baseInteraction A xxxx Hoogsteen  A xxxx SugarEdge Trans  
#baseInteraction A xxxx HelicalStackingA3 A xxxx HelicalStackingA5 Cis