NVT sim; bringing NH3 and CH3Cl together (no rxn)
&colvar
  cv_type = 'LCOD',             ! CV is linear comb. of dists.
  cv_ni   = 4,                  ! Number of atoms involved
  cv_i    = 5, 9, 5, 1,         ! The atom numbers involved
  cv_nr   = 2,                  ! Number of params (coeffs in LCOD)
  cv_r    = 1.0, -1.0,          ! CV: R = (+1)r_{break} + (-1)r_{formed}
  npath   = 2,                  ! Number of elements in path variable
  path    = -3, -2,             ! Where to start/end CV scan
  nharm   = 1,                  ! If 1, then constant constraint
  harm    = 80.0,               ! The harmonic constraint
/