colvarsTrajFrequency 100 colvar { name swarms_phi dihedral { group1 { atomNumbers 5 } group2 { atomNumbers 7 } group3 { atomNumbers 9 } group4 { atomNumbers 15 } } } harmonic { name bias_swarms_phi colvars swarms_phi centers 7.5 forceConstant 0.0 } colvar { name swarms_psi dihedral { group1 { atomNumbers 7 } group2 { atomNumbers 9 } group3 { atomNumbers 15 } group4 { atomNumbers 17 } } } harmonic { name bias_swarms_psi colvars swarms_psi centers -13.5 forceConstant 0.00 } colvar { name swarms_theta dihedral { group1 { atomNumbers 6 } group2 { atomNumbers 5 } group3 { atomNumbers 7 } group4 { atomNumbers 9 } } } harmonic { name bias_swarms_theta colvars swarms_theta centers 0.0 forceConstant 0.00 } colvar { name swarms_zeta dihedral { group1 { atomNumbers 16 } group2 { atomNumbers 15 } group3 { atomNumbers 17 } group4 { atomNumbers 19 } } } harmonic { name bias_swarms_zeta colvars swarms_zeta centers 0.0 forceConstant 0.00 } colvar { name molecular_position distance { group1 { atomNumbers 9 } group2 { dummyAtom (0.0, 0.0, 0.0) } } } harmonic { name bias_molecular_position colvars molecular_position centers 0.0 forceConstant 100.0 } colvar { name molecular_orientation distanceDir { group1 { atomNumbers 9 } group2 { atomNumbers 11 } } } harmonic { name bias_molecular_orientation colvars molecular_orientation centers (0.0, 1.0, 0.0) forceConstant 100.0 } colvar { name molecular_rotation distanceZ { main { atomNumbers 10 } ref { atomNumbers 9 } axis (1.0, 0.0, 0.0) } } harmonic { name bias_molecular_rotation colvars molecular_rotation centers 0.0 forceConstant 100.0 }