colvarsTrajFrequency      1000   
colvarsRestartFrequency   1000  

colvar {
  name DO
  lowerBoundary -40
  upperBoundary 40
  lowerWall -40
  upperWall 40
  lowerwallconstant 3
  upperwallconstant 3
  width 1.0
  distanceZ {
    main {
      atomsFile atomfile/DNMA.pdb
      atomsCol B
      atomsColValue 1.0
    }
    ref {
      psfSegID PROA
      atomNameResidueRange {CA 1-340}
    }
    axis {(0, 0, 1)}
  }
}


metadynamics {
   name     meta
   colvars  DO
   hillWeight              0.2
   newHillFrequency        1000
   writeHillsTrajectory    on
   hillwidth               0.2
   
   wellTempered            on
   biasTemperature         4000

   multipleReplicas on
   replicasRegistry shared-folder/mymtd-replicas.txt
   replicaUpdateFrequency 50000

}

colvar {
   name restrain01

   width 1.0

   lowerboundary   0.0
   upperboundary   20.0

   lowerWall 0
   upperWall 20.0

   lowerwallconstant 100.0
   upperwallconstant 100.0

   distanceXY {
forceNoPBC yes
      main {
        atomnumbers {5081 5082 5083 5084 5085 5086 5087 5088 5089 5090 5091 5092 5093 5094 5095 5096 5097 5098 5099 5100 5101 5102 5103 5104}
      }
      ref {
        psfSegID  PROA
        atomNameResidueRange CA 1-340

        }
      axis  {(-0.09950371902099892, 0.0, 0.9950371902099892)}
}
}


