setDefaultMDParameters
baseInteraction Y 26 WatsonCrick Y 44 WatsonCrick Cis
baseInteraction Y 27 WatsonCrick Y 43 WatsonCrick Cis
baseInteraction Y 28 WatsonCrick Y 42 WatsonCrick Cis
baseInteraction Y 29 WatsonCrick Y 41 WatsonCrick Cis
baseInteraction Y 30 WatsonCrick Y 40 WatsonCrick Cis
#baseInteraction Y 25 HelicalStackingA3 Y 26 HelicalStackingA5 Cis
#baseInteraction Y 26 HelicalStackingA3 Y 27 HelicalStackingA5 Cis
#baseInteraction Y 27 HelicalStackingA3 Y 28 HelicalStackingA5 Cis
baseInteraction Y 34 WatsonCrick X 21 WatsonCrick Cis
baseInteraction Y 35 WatsonCrick X 20 WatsonCrick Cis
baseInteraction Y 36 WatsonCrick X 19 WatsonCrick Cis
#baseInteraction Y 34 HelicalStackingA3 Y 35 HelicalStackingA5 Cis
#baseInteraction X 19 HelicalStackingA3 X 20 HelicalStackingA5 Cis

mobilizer Rigid X 12 22
mobilizer Rigid Y 1 75
mobilizer Default Y 26 27
mobilizer Default Y 41 44
mobilizer Default Y 33 36
mobilizer Default X 19 21


rootMobilizer Y Weld
rootMobilizer X Weld



constraint Y 1 C4' Weld Y 75 C4'
constraint Y 44 C4' Weld Y 10 C4'
constrainToGround Y 45
constrainToGround X 18


includeAllNonBondAtomsInResidues Y 10 10
includeAllNonBondAtomsInResidues Y 25 25
includeAllNonBondAtomsInResidues Y 26 26
includeAllNonBondAtomsInResidues Y 27 27
includeAllNonBondAtomsInResidues Y 41 41
includeAllNonBondAtomsInResidues Y 42 42
includeAllNonBondAtomsInResidues Y 43 43
includeAllNonBondAtomsInResidues Y 44 44
includeAllNonBondAtomsInResidues Y 31 31
includeAllNonBondAtomsInResidues Y 32 32
includeAllNonBondAtomsInResidues Y 33 33
includeAllNonBondAtomsInResidues Y 34 34
includeAllNonBondAtomsInResidues Y 35 35
includeAllNonBondAtomsInResidues Y 36 36
includeAllNonBondAtomsInResidues Y 37 37
includeAllNonBondAtomsInResidues Y 38 38
includeAllNonBondAtomsInResidues X 19 19
includeAllNonBondAtomsInResidues X 20 20
includeAllNonBondAtomsInResidues X 21 21
includeAllNonBondAtomsInResidues X 22 22




scrubberPeriod 40.0
temperature 10.0
reportingInterval 1.0
firstStage 0
lastStage 1
twoTransformForceMultiplier 10.0
removeRigidBodyMomentum False
setInitialVelocities False
smallGroupInertiaMultiplier 1.0
dutyCycle 1.0