# In this example, we create a hairpin with a three base pair stem and a four base loop.
# You can compare this to the tetraloop found in the large subunit of the yeast mitochondrial ribosome, PDB ID 5MRC, residues 2639 to 2648.

#sequence
RNA A 2656     UACGUAAGUA

# stages
firstStage 1 
lastStage 1

#general simulation parameters
# This is a multiplying factor for the baseInteraction forces:
baseInteractionScaleFactor     200
# Simulation time = reportingInterval * numReportingIntervals :
reportingInterval 4.0
numReportingIntervals 10
temperature 10 

nucleicAcidDuplex A 2656 2658 A 2665 2663

# Or, equivalently:
#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

# Turn on MD forces (incl. electrostatic and Lennard Jones forces)
setDefaultMDParameters