Higher-order correlated calculations based on fragment molecular orbital scheme

Mochizuki, Yuji; Yamashita, Katsumi; Nakano, Tatsuya; Okiyama, Yoshio; Fukuzawa, Kaori; Taguchi, Naoki; Tanaka, Shigenori

doi:10.1007/s00214-011-1036-3

Cited by 87 publications

(55 citation statements)

References 147 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additional review of S66 by Riley et al 42 for MP2, SCS-MP2, and SCS-S66-MP2 [S66-trained SCS(MI)-MP2] considered local and explicitly correlated variations on MP2. While the present work also deals with MP2-F12-and CC-F12-based methods and incorporates density-fitting where available, many further promising algorithmic approaches to reducing the computational cost of CCSD(T) such as local, 43,44 fragment, 45,46 limited virtual orbital space, 47,48 domain-based pair-natural orbitals, 49 and tensor hypercontraction 50 are not touched upon.…”

Section: Mp2mentioning

confidence: 99%

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

Burns

Marshall

Sherrill

2014

The Journal of Chemical Physics

112

View full text Add to dashboard Cite

A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.

show abstract

Section: Mp2mentioning

confidence: 99%

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

Burns

Marshall

Sherrill

2014

The Journal of Chemical Physics

112

View full text Add to dashboard Cite

show abstract

“…The most general approach, however, is to use quantum‐mechanical (QM) calculations, as these are able to treat all systems in an unbiased manner and can be systematically improved . Unfortunately, a level of theory that would guarantee high accuracy, such as coupled cluster with singles, doubles, and perturbative triples (CCSD(T)), is very computationally expensive and usually beyond reach for protein–ligand systems, although such calculations based on fragmentation are emerging . Even second‐order Møller–Plesset (MP2) calculations are relatively rare …”

Section: Introductionmentioning

confidence: 99%

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

2015

View full text Add to dashboard Cite

The most general way to improve the accuracy of binding-affinity calculations for protein-ligand systems is to use quantum-mechanical (QM) methods together with rigorous alchemical-perturbation (AP) methods. We explore this approach by calculating the relative binding free energy of two synthetic disaccharides binding to galectin-3 at a reasonably high QM level (dispersion-corrected density functional theory with a triple-zeta basis set) and with a sufficiently large QM system to include all short-range interactions with the ligand (744-748 atoms). The rest of the protein is treated as a collection of atomic multipoles (up to quadrupoles) and polarizabilities. Several methods for evaluating the binding free energy from the 3600 QM calculations are investigated in terms of stability and accuracy. In particular, methods using QM calculations only at the endpoints of the transformation are compared with the recently proposed non-Boltzmann Bennett acceptance ratio (NBB) method that uses QM calculations at several stages of the transformation. Unfortunately, none of the rigorous approaches give sufficient statistical precision. However, a novel approximate method, involving the direct use of QM energies in the Bennett acceptance ratio method, gives similar results as NBB but with better precision, ∼3 kJ/mol. The statistical error can be further reduced by performing a greater number of QM calculations.

show abstract

“…In addition, the FMO method is suitable for parallel computing because the monomer and dimer calculations are completely independent from each other. This method has been extended to several electron correlation methods including MP2, third‐order Møller–Plesset perturbation (MP3) theory, CC (including fourth‐order Møller–Plesset perturbation (MP4) theory), local MP2 and configuration interaction singles and perturbative doubles (CIS(D)) . An example of FMO calculations including the electron correlation was reported by Mochizuki et al In that work, the FMO‐MP3 calculations of a large biomolecular system, which contains more than 2000 amino acid residues, were completed within 6 h using 1024 vector processors.…”

Section: Introductionmentioning

confidence: 99%

“…The usefulness of MP2.5 has also been demonstrated . In the FMO context, Yamada et al adopted the MP2.5 method to evaluate the interaction energies among base moieties of DNA models, in comparison with the reference values of FMO‐CCSD(T) . Certainly, MP2.5 in the FMO calculations should be attractive, however the cost of the MP3 part could still be time‐consuming for routine usage as long as the regular ERIs are used in integral processing.…”

Section: Introductionmentioning

confidence: 99%

RI‐MP3 calculations of biomolecules based on the fragment molecular orbital method

2018

Self Cite

View full text Add to dashboard Cite

In this study, the third‐order Møller–Plesset perturbation (MP3) theory using the resolution of the identity (RI) approximation was combined with the fragment molecular orbital (FMO) method to efficiently calculate a high‐order electron correlation energy of biomolecular systems. We developed a new algorithm for the RI‐MP3 calculation, which can be used with the FMO scheme. After test calculations using a small molecule, the FMO‐RI‐MP3 calculations were performed for two biomolecular systems comprising a protein and a ligand. The computational cost of these calculations was only around 5 and 4 times higher than those of the FMO‐RHF calculations. The error associated with the RI approximation was around 2.0% of the third‐order correlation contribution to the total energy. However, the RI approximation error in the interaction energy between the protein and ligand molecule was insignificantly small, which reflected the negligible error in the inter fragment interaction energy. © 2018 Wiley Periodicals, Inc.

show abstract

Higher-order correlated calculations based on fragment molecular orbital scheme

Cited by 87 publications

References 147 publications

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

RI‐MP3 calculations of biomolecules based on the fragment molecular orbital method

Contact Info

Product

Resources

About