Conformational Search

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parameter	default	description
conformer_search	0	1: perform conformational search, 0: do not.
conf_grid *	3	The angular grid for dihedrals in the conformational search, angle = 360 / grid.
semi_emp_conformer_search	0	Whether to carry out a semiempirical optimization prior to L1.
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
me	0	1: automatically run the master equation calculations, 0: do not.
rotation_restart	3	Number of hindered internal rotor calculation restarts in case a lower energy point is found along a scan.
max_dihed *	5	Maximum number of diherals 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.
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.
min_bond_break	2	In the combinatorial reaction search, this parameter specifies the minimum number of bonds to be broken per reaction.
max_bond_break	3	In the combinatorial reaction search, this parameter specifies the maximum number of bonds to be broken per reaction.
comb_molec	1	In the combinatorial reaction search, allow for molecular pathways.
comb_rad	1	In the combinatorial reaction search, allow for radical pathways.
comb_lone	1	In the combinatorial reaction search, allow for reactions involving lone electron pairs.
comb_pi	1	In the combinatorial reaction search, allow for reactions involving pi-electrons.
break_valence	1	In the combinatorial reaction search, allow for atom valences to be altered.
one_reaction_comb	0	Search for a specific reaction using the combinatorial algorithm.
one_reaction_fam	0	Search for a specific reactions using the reaction family algorithm.
ringrange	[3, 9]	For cyclic transition states search for cycle sizes within this range.
barrierless_saddle	{}	Prescribe which bonds to be broken for which species to search for the barrierless_saddle channel in the following form: {chemid1: [[atom1, atom2], [atom3, atom4], ...], [chemid2: [..]]}. In this case for species 1 defined by the chemid two barrierless channels are searched for, the breaking of the atom1 -- atom2 and atom3 -- atom4 bonds. For species 2 further requests can be provided. Note that the family can only be requested once the chemids and the atom numbers are known, such as on a restart.
barrierless_saddle_start	2.0	The starting distance for the scan in the barrierless_saddle family in Angstrom.
imagfreq_threshold	50.	The largest imaginary frequency (need a positive number) that is still accepted as valid for minima. In the master equation the frequency is flipped, and a warning is given in the log file.

While KinBot is fully restartable, some parameters cannot be changed upon restart without compromising the calculations. These are marked with an asterisk (*).