#############################################################
## Collective Variables                                    ##
#############################################################

# Global parameters
colvarsTrajFrequency 500

colvar {
    name q1_6
    orientation {
	atoms {
	    psfSegID PROA PROA PROA PROA PROA PROA
	    atomNameResidueRange { CA 20-54 }
	    atomNameResidueRange { CA 66-86 }
	    atomNameResidueRange { CA 94-112 }
	    atomNameResidueRange { CA 122-148 }
	    atomNameResidueRange { CA 158-183 }
	    atomNameResidueRange { CA 190-207 }
	}
	refPositionsFile ../../system/eq.pdb
    }
}

colvar {
    name q7_12
    orientation {
	atoms {
	    psfSegID PROB PROB PROB PROB PROB PROB
	    atomNameResidueRange { CA 253-282 }
	    atomNameResidueRange { CA 293-316 }
	    atomNameResidueRange { CA 322-341 }
	    atomNameResidueRange { CA 351-374 }
	    atomNameResidueRange { CA 382-409 }
	    atomNameResidueRange { CA 415-448 }
	}
	refPositionsFile ../../system/eq.pdb
    }
}

harmonic {
    name harm
    colvars { q1_6 q7_12 }
    # initial values
    centers { ( 1 , 0 , 0 , 0 )  ( 1 , 0 , 0 , 0 ) }
    # target values; can be determined by "vmd -e axis.tcl"
    targetCenters { ( 0.984807753012208 , -0.06348657931818914 , 0.16078048239637263 , 0.016515947141669058 ) ( 0.984807753012208 , 0.06348657931818914 , -0.16078048239637263 , -0.016515947141669058 ) }
    # force constant in kcal/(mol*rad^2); note: 3,286 kcal/(mol*rad^2) =~ 1 kcal/(mol*deg^2)
    forceConstant 10000
    # steering protocol time
    targetNumSteps 2000000
    # calculate work
    outputAccumulatedWork on
}