Abstract
When dealing with large biological systems speed determines the utility of the computational method. Therefore in order to bring quantum-mechanical (QM) methods to computational studies of biomolecules it is necessary to significantly reduce their resource requirement. In this light semiempirical QM methods are particularly encouraging because of their modest computational cost combined with potentially high accuracy. However, even semiempirical methods are frequently found to be too demanding for typical biological applications which require extensive conformational sampling. Significant speed up is obtained in the linear scaling LocalSCF method which is based on the variational finite localized molecular orbital (VFL) approximation. The VFL provides an approximate variational solution to the Hartree-Fock-Roothaan equation by seeking the density matrix and energy of the system in the basis of compact molecular orbitals using constrained atomic orbital expansion (CMO). Gradual release of the expansion constraints leads to determination of the theoretically most localized solution under small non-orthogonality of CMOs. Validation tests confirm good agreement of the LocalSCF method with matrix diagonalization results on partial atomic charges, dipole moment, conformational energies, and geometry gradients while the method exhibits low computer memory and CPU time requirements. We observe stable dynamics when using the LocalSCF method.
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Abbreviations
- AM1:
-
Austin model 1
- AO:
-
Atomic orbital
- B3LYP:
-
Becke 3-term correlation, Lee-Yang-Parr exchange functional
- CC:
-
Coupled cluster
- CI:
-
Configuration interaction
- CMO:
-
Constrained expansion molecular orbital
- CPU:
-
Central processing unit
- DFT:
-
Density functional theory;
- HF/6-31G*:
-
Hartree-Fock method using Pople 6-31G* basis set
- HOF:
-
Heat of formation
- LMO:
-
Localized molecular orbital
- LocalSCF:
-
Local self consistent field
- MD:
-
Molecular dynamics
- MO:
-
Molecular orbital
- MP2:
-
Second-order Moller-Plesset perturbation theory
- NDDO:
-
Neglect of diatomic differential overlap
- NPT:
-
Constant number of particles, pressure, and temperature
- NVE:
-
Constant number of particles, volume, and energy
- NVT:
-
Constant number of particles, volume and temperature
- PBC:
-
Periodic boundary condition
- PM3:
-
Parametric method 3
- PM5:
-
Parametric method 5
- QM:
-
Quantum mechanics
- RAM:
-
Random access memory
- SBP:
-
Spherical boundary potential
- SCF:
-
Self-consistent field
- VFL:
-
Variational finite localized molecular orbital approximation
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Panczakiewicz, A., Anisimov, V.M. (2011). The Linear Scaling Semiempirical LocalSCF Method and the Variational Finite LMO Approximation. In: Zalesny, R., Papadopoulos, M., Mezey, P., Leszczynski, J. (eds) Linear-Scaling Techniques in Computational Chemistry and Physics. Challenges and Advances in Computational Chemistry and Physics, vol 13. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2853-2_15
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