parameters /home/Liam/programs/i3Drefine/software/3Drefine/parameters
#
#
# Weights for the energy terms
bondEnergy weight 0.10
LennardJonesCa weight 0.2
LennardJones weight 0.00
angleEnergy weight 2.0
planeEnergy weight 10.0
twoTorsionsEnergy weight 1.0
flatRamachEnergy weight 6
propensityTorsionEnergy weight 1.0
solvateEnergy weight 10.0
outOfPlaneEnergy weight 100.0
alphaAngleEnergy weight 1.0 
alphaTorsionEnergy weight 1.0 
hydrogenBonds weight 0.001
hydrogenBondsPairs weight 0.1
hydrogenBondsPlane weight 0
hydrogenBondsAngles weight 100
cAlphaHydrogenBonds weight 0.0
cAlphaHOtorsins weight 0.0
tetherEnergy weight 10.0
templateEnergy weight 10.0
electrostatics weight 0.1
electrostatics dielectricConstant 4
ramachandranSidechain weight 10
atomicPairwisePMFSumma weight 1
compositePropensity weight 10

# Inflate parameters
inflateEnergy weight 0.1
inflateEnergy RmsTarget 1


# Minimization parameters - full minimization
minimize maxSteps 200000
minimize tolerance 0.1
minimize reportEvery 200

# Minimization parameters - short relaxation
relax tolerance 0.1
relax maxSteps 6000
relax reportEvery 200

# MCM parameters
mcmPerturbation tolerance 0.01
mcmPerturbation maxSteps 200000
mcmPerturbation reportEvery 200
MCM initialTemperature 10
MCM finalTemperature 0.01
MCM maxSteps 10


# This command tels the program to use our approximated arcCosinus which is ~4 times 
# faster than the one in the StrictMath library. 
useFastArcCos
dresserFragments fragments5.txt
rotamerLibrary bbdep02.May.sortlib

#Misc.
seed 4
corpusFileName parameters/finalCorpus.txt
maxRunTime 10000
