In principle, the same effect of constrained optimization using fixed atoms can be achieved instead using soft harmonic confining potentials of the form
This represents an external potential that confines the th atom (having coordinates ) around the position . In applications to cluster models of enzymes (as a low-cost alternative to QM/MM simulations), it is necessary to lock certain atoms at their crystallographic positions in order to relax the geometry (in the gas phase or in continuum solvent) without collapsing the active-site model.1031, 249
Use of a confining potential allows this optimization to proceed in an unconstrained manner, using delocalized internal coordinates (rather than Cartesian coordinates) for efficiency, yet achieves the same effect as the traditional fixed-atom approach that is widely used in cluster models of enzymatic reactions.1031 Moreover, the use of harmonic confining potentials does not result in imaginary frequencies that can plague fixed-atom optimizations, making it straightforward to compute zero-point vibrational corrections.249
Harmonic confining potentials are activated by setting the $rem variable HARM_OPT to true, listing the indices of the confined atoms in the $harmonic_opt section and their corresponding equilibrium positions () in the $coords section.
$molecule 0 1 C 2.2847229688 -0.3069830925 -0.2968221397 C 0.9156471557 0.1503924513 0.1693932675 N -0.0576877706 -0.7876400788 0.0645249649 H 2.9837678662 0.5043669375 -0.1693203557 H 2.2497378474 -0.5929607607 -1.3422589452 H 2.6126794028 -1.1626691284 0.2825927880 O 0.6966207559 1.2669942030 0.6077661092 C -1.4350712383 -0.4874947903 0.4670886412 H 0.1463602169 -1.6783001309 -0.3307859180 C -2.1768099264 0.3412632672 -0.5936684676 H -1.3995705380 0.0636682083 1.3955334557 H -1.9421824240 -1.4270154508 0.6422037013 H -1.6624625664 1.2829541077 -0.7297597438 H -3.1943263155 0.5415731987 -0.2762358302 H -2.2051967614 -0.1880845317 -1.5391034623 $end $rem JOBTYPE OPT METHOD HF BASIS 3-21G SYM_IGNORE true NO_REORIENT true HARM_OPT 1 ! Turn on harmonic confining potential HOATOMS 2 ! No. of confined atoms HARM_FORCE 450 ! Force constant of the potential $end $harmonic_opt 1 10 ! indices of the confined atoms $end $coords !coordinates of confined atoms C1 2.2847229688 -0.3069830925 -0.2968221397 C10 -2.1768099264 0.3412632672 -0.5936684676 $end