Colvars: Unable to restrict rotation and translation along y and z axes

From: Sourav Ray (souravray90_at_gmail.com)
Date: Wed May 18 2016 - 07:22:00 CDT

Hello

I am trying to vary the distance between two carbon nanotubes along x-axis.
Additionally, I would like to restrict any rotation, whatsoever, and
translation along y and z axes. I am using "Distancedir" to restrict
translation for both the nano-tubes along y and z axes and "orient" to
restrict rotation with "harmonic" constraint. However, I am not getting the
desired effect. Please find the colvars script below:

colvarsTrajFrequency 10000
colvarsRestartFrequency 10000

colvar {

  name cntdis
  width 0.1
  lowerboundary 12.0
  upperboundary 20.0
  lowerwallconstant 100.0
  upperwallconstant 100.0

  distance {
    group1 {
    atomnumbersrange { 1-364 }
    }

    group2 {
    atomnumbersrange { 365-728 }
   }

}
}

colvar {
  name orient

  width 0.1 # distance between quaternions is from 0 to pi/2, so small
fluctuations are significant

  orientation {
    atoms {
        atomNumbersrange { 1-728 }
enableForces off
    }
    refPositionsFile ../ref.pdb # Fetch initial positions from this file
  }
}

colvar {

  name ztrans1
  width 0.1

  distancedir {
    group1 {
    atomnumbersrange { 1-364 }
    }

    group2 {
    dummyatom (-6.5,0,0)
   }
  }
}

colvar {

  name ztrans2
  width 0.1

  distancedir {
    group1 {
    atomnumbersrange { 365-728 }
    }

    group2 {
    dummyatom (6.5,0,0)
   }
  }

harmonic {
colvars orient ztrans1 ztrans2
centers (1,0,0,0) (1,0,0) (1,0,0)
forceconstant 10.0
}
metadynamics {
colvars cntdis
hillWidth 2
hillWeight 0.5
newHillFrequency 100
}

Please let me know if someone has any insight regarding the same.

Regards
Sourav


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