# scalar distance (norm of "dist") between the centers of mass of two groups
colvar {
    name r

    width 0.25

    lowerBoundary 0.0
    upperBoundary 20.0

    lowerwallconstant 100.0
    upperwallconstant 100.0

    distance {

       forceNoPBC yes
       group1 {
         atomNumbers { 1739 }
       }
       group2 {
         atomNumbers { 191 216 217 250 251 274 }
       }

    }
}


colvar {
  name RMSD

  width 0.5  # typical RMSD fluctuation set to 0.5 Angstrom

  rmsd {
    atoms {
      atomsFile restrain.ref
      atomsCol O
      atomsColValue 1.0 
    }
    refPositionsFile step3_charmm2namd.pdb  # Fetch initial positions from this file
  }
}

colvar {
   name theta

   width 1.0

   lowerBoundary 0.0
   upperBoundary 180.0
   lowerwallconstant 0.2
   upperwallconstant 0.2

   polarTheta {
     atoms {
       atomsfile  new_frame.ref
       atomsCol   O
       atomsColValue 2.0

       rotateReference off
       centerReference on
       fittingGroup {
          atomsfile  new_frame.ref
          atomsCol   O
          atomsColValue 1.0
       }
       refPositionsFile   step3_charmm2namd.pdb
     }
   }
}


colvar {
   name phi

   width 1.0

   lowerBoundary -179.0
   upperBoundary 179.0
   lowerwallconstant 0.2
   upperwallconstant 0.2

   polarPhi {
     atoms {
       atomsfile  new_frame.ref
       atomsCol   O
       atomsColValue 2.0

       rotateReference off
       centerReference on
       fittingGroup {
          atomsfile  new_frame.ref
          atomsCol   O
          atomsColValue 1.0
       }
       refPositionsFile   step3_charmm2namd.pdb
     }
   }
}