Conformers and Rotors

Conformers and rotors

Conformational search

parameter	default	description
conformer_search	0	1: perform conformational search, 0: do not.
allow_l2_without_conf	0	Expert option. high_level normally requires conformer_search to be 1, so that L2 refines the lowest conformer rather than an arbitrary one. Set to 1 to lift that requirement, for instance when L1 was carried out elsewhere, with another code or level of theory, and KinBot is only asked to run L2 on the supplied geometries. The L2 energies are then those of whichever conformer is given, and are not guaranteed to belong to the lowest one. A warning is written to the log file whenever this is used.
conf_grid *	3	The angular grid for dihedrals in the conformational search, angle = 360 / grid.
difference_threshold	0.1	Energy difference (kcal/mol) below which two conformers are considered to be the same.
l0_conformer_search	0	1: run a preliminary, cheap conformer search (L0) for wells before the L1 search, and pass only the lowest conformers to L1. Requires conformer_search: 1. The level is l0_method with the same code, or l0_profile (see Quantum Chemistry). Not applied to transition states. Formerly semi_emp_conformer_search.
l0_method	"am1"	Method of the L0 search when no l0_profile is given. Formerly semi_emp_method.
l0_max_dihed *	5	Maximum number of dihedrals for which the L0 search is exhaustive. Formerly max_dihed_semi_emp.
l0_random_conf *	500	Number of random L0 conformers beyond that. Formerly random_conf_semi_emp.
l0_conformer_threshold	5	Energy window (kcal/mol) above the lowest L0 conformer within which conformers are passed to L1. Formerly semi_emp_confomer_threshold.
max_dihed *	5	Maximum number of dihedrals for which exhaustive conformation search is done.
random_conf *	500	Number of random conformers in case no exhaustive search is done.
flat_ring_dih_angle *	5.0	If the dihedral angle between four atoms in a ring are smaller than this value (in degrees), then that section of the ring is considered flat, and is not considered in the ring conformer search algorithm.

The old L0 names are still accepted with a deprecation warning; giving an old and a new name with different values is an error.

On a restart, a finished conformer search is not repeated: KinBot recognises it by the files conf/<name>_low.<ext> (.log Gaussian, .out Q-Chem, _sella.log ORCA/FairChem/Sella) and the last conformer's output, and reads the selected conformer from kinbot.db. The file is removed when a hindered-rotor scan finds a lower conformer, which forces a new search.

Hindered rotors

parameter	default	description
rotor_scan	0	1: perform 1D hindered rotor scans, 0: do not.
nrotation *	12	Number of energy evaluations along a 1D hindered rotor scan.
free_rotor_thrs	0.1	Threshold to consider a rotor free. This is the maximum barrier in kcal/mol.
plot_hir_profiles	0	Make figures of the HIR profiles
rotation_restart	3	Number of hindered internal rotor calculation restarts in case a lower energy point is found along a scan.
rotor_0_test	1	1: if the first point of a rotor scan (the unrotated geometry) differs by more than 0.1 kcal/mol from the optimized energy, usually a sign of SCF convergence problems, switch off the hindered rotors of that stationary point. 0: do not check.
rigid_hir	0	1: rigid rotor scans, i.e. single points along the dihedral without relaxing the rest of the structure. 0: relaxed scans.
hir_maxcycle	none	Maximum number of optimization cycles at each point of the relaxed rotor scans of saddle points (Gaussian MaxCycle). Without it, Gaussian's default applies.

Multi-conformer TST

parameter	default	description
multi_conf_tst	0	Set up a multi-conformer TST calculation, useful for low-temperature, e.g., atmospheric chemistry.
multi_conf_tst_temp	300	Temperature (in K) for which the conformers are considered if multi_conf_tst is active.
multi_conf_tst_boltz	0.05	Fractional abundance as in exp(-E/RT), where T is multi_conf_tst_temp, above which a conformer is discarded.
print_conf	0	If set to 1, KinBot prints the list of unique conformers into the log file. Can take longer on restarts in case of many conformers. If multi_conf_tst is 1, it is always printed. Note that in that case only the ones determined by multi_conf_tst_temp and multi_conf_tst_boltz are considered.

Parameters marked with an asterisk (*) must not change when a run is restarted, see Restarting.