colvarsTrajFrequency 1000 colvar { name length outputAppliedForce off distance { group1 { atomsfile atomdefine1.pdb # Select biased atoms from this file atomsCol B # based on column beta atomsColValue 1 # atoms flagged with 1 } group2 { atomsfile atomdefine2.pdb # Select biased atoms from this file atomsCol B # based on column beta atomsColValue 2 # atoms flagged with 2 } } } harmonic { name lenpot colvars length forceConstant 8 # in kcal/mol/A^2 centers 26.8 # go from 25 Angstrom RMSD... targetCenters 5.0 # ... to 1 Angstrom targetNumSteps 500000 # in 500000 MD steps outputCenters no # outputAccumulatedWork yes # keep track of how much energy will be added #writeTIPMF yes }