lammps/examples/USER/colvars/peptide.colvars

# collective variable example: monitor distances

colvarsTrajFrequency 1 # output every 10 steps
colvarsRestartFrequency 1000

colvar {
  name one

  distance {
    group1 {
      atomNumbers 2 4 5 6
    }
    group2 {
      atomNumbers 37
    }
  }
}

colvar {
  name two

  distance {
    group1 {
      atomNumbers 80 82 83 84
    }
    group2 {
      atomNumbers 37
    }
  }
}

harmonic {
  name h_pot
  colvars one two
  centers 10.00 10.0
  forceConstant 100.0
}