Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems
- 15 December 2000
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 113 (23) , 10512-10523
- https://doi.org/10.1063/1.1323257
Abstract
We present a detailed analysis of the performance of the semiempirical divide and conquer method as compared with standard semiempirical MO calculations. The influence of different subsetting schemes involving dual buffer regions on the magnitude of the errors in energies and computational cost of the calculations are discussed. In addition, the results of geometry optimizations on several protein systems (453 to 4088 atoms) driven by a quasi-Newton algorithm are also presented. These results indicate that the divide and conquer approach gives reliable energies and gradients and suggest that protein geometry optimization using semiempirical methods can be routinely feasible using current computational resources.Keywords
This publication has 41 references indexed in Scilit:
- Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical HamiltonianThe Journal of Chemical Physics, 2000
- Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling Electronic Structure MethodsPhysical Review Letters, 1998
- High-Resolution Structure (1.33 Å) of a HEW Lysozyme Tetragonal Crystal Grown in the APCF Apparatus. Data and Structural Comparison with a Crystal Grown under Microgravity from SpaceHab-01 MissionActa Crystallographica Section D-Biological Crystallography, 1996
- A density-matrix divide-and-conquer approach for electronic structure calculations of large moleculesThe Journal of Chemical Physics, 1995
- Generalization of the density-matrix method to a nonorthogonal basisPhysical Review B, 1994
- Amino acids of the recombinant kringle 1 domain of human plasminogen that stabilize its interaction with .omega.-amino acidsBiochemistry, 1993
- Atomic Resolution (0·83 Å) Crystal Structure of the Hydrophobic Protein Crambin at 130 KJournal of Molecular Biology, 1993
- Direct calculation of electron density in density-functional theoryPhysical Review Letters, 1991
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983
- Some Recent Advances in Density Matrix TheoryReviews of Modern Physics, 1960