The numerical accuracy of linear scaling semiempirical methods LocalSCF and MOZYME is analyzed in comparison to conventional matrix diagonalization with respect to a variety of molecular properties including conformational energy, dipole moment, atomic charges, and bond orders. Major semiempirical MNDO, AM1, PM3, and PM5 Hamiltonians were considered in the study. As the numerical tests demonstrate, both LocalSCF and MOZYME reasonably reproduce matrix diagonalization results with the deviations being below the accuracy of semiempirical methods. However, the economical LocalSCF memory consumption and faster calculations are more beneficial for the quantum-mechanical modeling of large biological systems. The computational performance of the LocalSCF method is tested on the conformational energy calculation of a series of molecular dynamics snapshots of insulin in a large box of water.
ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry