sequence A      AA               
sequence B      AA               
resetBases B 1
-PRIOR 0
#-SQ B     AAAAAAAAACCCCUUUUUUUUU   
addNASTForces 0
periodicallyUpdateParameters 0
backboneOxygenGlobalCoulombScaleFactor 1  
backboneOxygenGlobalVdwScaleFactor 1  
addBackboneOxygenForces 0
numMagnesiumIons 10
addBackboneOxygenForces 0
maxReportingIntervals  500
reportingInterval .02
scrubberPeriod  4 
prioritize 0
setForceScrubber 0
lastStage 1 
# torsion = 2 rigid =3

leontisWesthofInFileName /Users/samuelflores/svn/tar-dynamics/hairpin-short/Base-interaction-parameters.4.csv

addHuntCrossleySpheres 0
piecewiseRigidify 0
loopBondMobility 1
helixBondMobility 3 
overallBondMobility 1
setOverallBondMobility 0
setLoopBondMobility 0
setForceAndStericScrubber 0
rigidifyFormedHelices 0
rigidifyTermini 0
weldToGround 0

-FRN A 7 
-FRN B 7 
#-FRN B 1 
firstStage 1 
cutoffRadius 4.0
readPreviousFrameFile 1
readInQVector 0
# -FS 1 
-T   50 1
#-T 2000 2
#-T 1000 3
#-T  500 4
#-T  250 5
#-T  125 6
-DC .5 20
-DC 1. 1
-DC 1. 5

-BP A 7 HelicalStacking A 8 HelicalStacking Cis 1
-BP B 7 HelicalStacking B 8 HelicalStacking Cis 1
# -BP A 8 WatsonCrick A 15 WatsonCrick Cis 1
# -BP A 9 WatsonCrick A 14 WatsonCrick Cis 1

# -BP B 7 WatsonCrick B 16 WatsonCrick Cis 1
# -BP B 8 WatsonCrick B 15 WatsonCrick Cis 1
# -BP B 9 WatsonCrick B 14 WatsonCrick Cis 1

# -BP A 10 Custom  B 10 Custom Cis 1
-BP A 8 WatsonCrick B 8 WatsonCrick Cis 1

globalCoulombScaleFactor 0.0 1 
globalVdwScaleFactor 0.0 1