1
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Stocks R, Palethorpe E, Barca GMJ. High-Performance Multi-GPU Analytic RI-MP2 Energy Gradients. J Chem Theory Comput 2024; 20:2505-2519. [PMID: 38456899 DOI: 10.1021/acs.jctc.3c01424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
This article presents a novel algorithm for the calculation of analytic energy gradients from second-order Møller-Plesset perturbation theory within the Resolution-of-the-Identity approximation (RI-MP2), which is designed to achieve high performance on clusters with multiple graphical processing units (GPUs). The algorithm uses GPUs for all major steps of the calculation, including integral generation, formation of all required intermediate tensors, solution of the Z-vector equation and gradient accumulation. The implementation in the EXtreme Scale Electronic Structure System (EXESS) software package includes a tailored, highly efficient, multistream scheduling system to hide CPU-GPU data transfer latencies and allows nodes with 8 A100 GPUs to operate at over 80% of theoretical peak floating-point performance. Comparative performance analysis shows a significant reduction in computational time relative to traditional multicore CPU-based methods, with our approach achieving up to a 95-fold speedup over the single-node performance of established software such as Q-Chem and ORCA. Additionally, we demonstrate that pairing our implementation with the molecular fragmentation framework in EXESS can drastically lower the computational scaling of RI-MP2 gradient calculations from quintic to subquadratic, enabling further substantial savings in runtime while retaining high numerical accuracy in the resulting gradients.
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Affiliation(s)
- Ryan Stocks
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Elise Palethorpe
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Giuseppe M J Barca
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
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2
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Nakata H, Kitoh-Nishioka H, Sakai W, Choi CH. Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation. J Chem Theory Comput 2023; 19:1517-1528. [PMID: 36757219 DOI: 10.1021/acs.jctc.2c01221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
A multiscale scheme (MLMS: Multi-Level Multi-Scale) to predict the ion mobility (μ) of amorphous organic semiconductors is proposed, which was successfully applied to the hole mobility predictions of 14 organic systems. An inverse relationship between μ and reorganization energy is observed due to local polaronic distortions. Another moderate inverse correlation between μ and distribution of site energy change exists, representing the effects of geometric flexibility. The former and the latter represent the intramolecular and intermolecular geometric effects, respectively. In addition, a linear correlation between transfer coupling and μ is observed, showing the importance of orbital overlaps between monomers. Especially, the highest hole mobility of C6-2TTN is due to its large transfer coupling. On the other hand, another high hole mobility of CBP turned out to come from the high first neighbor density (ρFND) of its first self-solvation, emphasizing the proper description of amorphous structural configurations with a sufficiently large number of monomers. In general, systems with either unusually high transfer coupling or high first neighbor density can potentially have high μ regardless of geometric effects. Especially, the newly suggested design parameter, ρFND, is pointing to a new direction as opposed to the traditional π-conjugation strategy.
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Affiliation(s)
- Hiroya Nakata
- Research Institute for Advanced Materials and Devices, Kyocera Corporation, 3-5-3 Hikaridai Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Hirotaka Kitoh-Nishioka
- Department of Energy and Materials, Faculty of Science and Engineering, Kindai University, 3 Chome-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Wakana Sakai
- Research Institute for Advanced Materials and Devices, Kyocera Corporation, 3-5-3 Hikaridai Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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3
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Nakata H, Fedorov DG. Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2023; 19:1276-1285. [PMID: 36753486 DOI: 10.1021/acs.jctc.2c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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4
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Liang Q, Yang J. Third-Order Many-Body Expansion of OSV-MP2 Wave Function for Low-Order Scaling Analytical Gradient Computation. J Chem Theory Comput 2021; 17:6841-6860. [PMID: 34704757 DOI: 10.1021/acs.jctc.1c00581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present a many-body expansion (MBE) formulation and implementation for efficient computation of analytical energy gradients from the orbital-specific-virtual second-order Møllet-Plesset perturbation theory (OSV-MP2) based on our earlier work (Zhou et al. J. Chem. Theory Comput. 2020, 16, 196-210). The third-order MBE(3) expansion of OSV-MP2 amplitudes and density matrices was developed to adopt the orbital-specific clustering and long-range termination schemes, which avoids term-by-term differentiations of the MBE energy bodies. We achieve better efficiency by exploiting the algorithmic sparsity that allows us to prune out insignificant fitting integrals and OSV relaxations. With these approximations, the present implementation is benchmarked on a range of molecules that show an economic scaling in the linear and quadratic regimes for computing MBE(3)-OSV-MP2 amplitude and gradient equations, respectively, and yields normal accuracy comparable to the original OSV-MP2 results. The MPI-3-based parallelism through shared memory one-sided communication is further developed for improving parallel scalability and memory accessibility by sorting the MBE(3) orbital clusters into independent tasks that are distributed on multiple processes across many nodes, supporting both global and local data locations in which selected MBE(3)-OSV-MP2 intermediates of different sizes are distinguished and accordingly placed. The accuracy and efficiency level of our MBE(3)-OSV-MP2 analytical gradient implementation is finally illustrated in two applications: we show that the subtle coordination structure differences of mechanically interlocked Cu-catenane complexes can be distinguished when tuning ligand lengths; and the porphycene molecular dynamics reveals the emergence of the vibrational signature arising from softened N-H stretching associated with hydrogen transfer, using an MP2 level of electron correlation and classical nuclei for the first time.
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Affiliation(s)
- Qiujiang Liang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
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5
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Ishikawa T. A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Galvez Vallejo JL, Westheimer B, Włoch M, Xu P, Zahariev F, Gordon MS. Recent developments in the general atomic and molecular electronic structure system. J Chem Phys 2020; 152:154102. [PMID: 32321259 DOI: 10.1063/5.0005188] [Citation(s) in RCA: 506] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Laura Carrington
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Jeffrey R Gour
- Microsoft, 15590 NE 31st St., Redmond, Washington 98052, USA
| | - Anastasia O Gunina
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Stephan Irle
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Karol Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sarom S Leang
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jesse J Lutz
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Spencer R Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Alistair P Rendell
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke B Roskop
- Cray Inc., a Hewlett Packard Enterprise Company, 2131 Lindau Ln #1000, Bloomington, Minnesota 55425, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ananta Tiwari
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Marta Włoch
- 530 Charlesina Dr., Rochester, Michigan 48306, USA
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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7
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Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method. Methods Mol Biol 2020. [PMID: 32016888 DOI: 10.1007/978-1-0716-0282-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent development of the fragment molecular orbital (FMO) method related to energy gradients, geometry optimization, transition state search, and chemical reaction mapping is summarized. The frozen domain formulation of FMO is introduced in detail, and the structure of related GAMESS input files for FMO is described.
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8
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Pham BQ, Gordon MS. Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model. J Chem Theory Comput 2020; 16:1039-1054. [PMID: 31899632 DOI: 10.1021/acs.jctc.9b01082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The fully analytic gradient of the second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity (RI) approximation in the fragment molecular orbital (FMO) framework is derived and implemented using a hybrid multilevel parallel programming model, a combination of the general distributed data interface (GDDI) and the OpenMP API. The FMO/MP2 analytic gradient contains three parts, i.e., the internal fragment component, the electrostatic potential (ESP) component, and the response terms. The RI approximation is applied to the internal fragment MP2 gradient term, whose MP2 densities and monomer MP2 Lagrangians are shared with the ESP and the response terms. The FMO/RI-MP2 analytic gradient implementation is validated against the numerical gradient (with errors ∼10-6-10-5 Hartree/Bohr) and the energy conservation in molecular dynamics (MD) simulations using NVE ensembles. The RI approximation introduces an error of ∼10-5 Hartree/Bohr with a speedup of 4.0-8.0× compared with the currently available GDDI FMO/MP2 gradient. The node linear scaling of the fragmentation framework due to multilevel parallelism is well-preserved and is demonstrated in single-point gradient calculations of large water clusters (e.g., 1120 and 2165 molecules) using 300-800 KNL compute nodes with a parallel efficiency of more than 90%.
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Affiliation(s)
- Buu Q Pham
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory , Iowa State University , Ames , Iowa 50011 , United States
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9
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Pham BQ, Gordon MS. Hybrid Distributed/Shared Memory Model for the RI-MP2 Method in the Fragment Molecular Orbital Framework. J Chem Theory Comput 2019; 15:5252-5258. [DOI: 10.1021/acs.jctc.9b00409] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Buu Q. Pham
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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11
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Liu J, Rana B, Liu KY, Herbert JM. Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics. J Phys Chem Lett 2019; 10:3877-3886. [PMID: 31251619 DOI: 10.1021/acs.jpclett.9b01214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.
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Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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12
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Ni Z, Wang Y, Li W, Pulay P, Li S. Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and Its Application to Geometry Optimizations of Large Systems. J Chem Theory Comput 2019; 15:3623-3634. [PMID: 31091102 DOI: 10.1021/acs.jctc.9b00259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient analytical energy gradient algorithm for the cluster-in-molecule (CIM) second order Møller-Plesset perturbation theory (MP2) method is presented. In our algorithm, the gradient contributions from the nonseparable term of the two-body density matrix on a given atom is extracted from calculations on a cluster constructed for this atom. The other terms in the CIM-MP2 energy gradient expression are evaluated by constructing the density matrices of the whole system with the contributions from all clusters constructed. For basis sets with diffuse functions, tight CIM parameters are necessary to obtain accurate gradients. Benchmark calculations show that the CIM-MP2 method can accurately reproduce the conventional MP2 gradients and geometries for larger systems. The optimized structure of a 174-atom oligopeptide using the CIM-MP2 method with the cc-pVDZ basis set is in good agreement with the corresponding crystal structure. The present CIM-MP2 gradient program can be used for optimizing the geometries of large systems with hundreds of atoms on ordinary workstations.
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Affiliation(s)
- Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China.,Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
| | - Peter Pulay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , P. R. China
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13
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Nishimoto Y, Fedorov DG. Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding. J Chem Phys 2018; 148:064115. [DOI: 10.1063/1.5012935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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14
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Blanco-Díaz EG, Vázquez-Montelongo EA, Cisneros GA, Castrejón-González EO. Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD. J Chem Phys 2018; 148:054303. [DOI: 10.1063/1.5017987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edgar G. Blanco-Díaz
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato 38010,
Mexico
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76206, USA
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15
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Song C, Martínez TJ. Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units. J Chem Phys 2017; 147:161723. [DOI: 10.1063/1.4997997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chenchen Song
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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16
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Fedorov DG. The fragment molecular orbital method: theoretical development, implementation in
GAMESS
, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1322] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD‐FMat)National Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
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17
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Bykov D, Kristensen K, Kjærgaard T. The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient. J Chem Phys 2016; 145:024106. [DOI: 10.1063/1.4956454] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dmytro Bykov
- Department of Chemistry, qLeap Center for Theoretical Chemistry, University of Aarhus, DK-8000 Århus C, Denmark
| | - Kasper Kristensen
- Department of Chemistry, qLeap Center for Theoretical Chemistry, University of Aarhus, DK-8000 Århus C, Denmark
| | - Thomas Kjærgaard
- Department of Chemistry, qLeap Center for Theoretical Chemistry, University of Aarhus, DK-8000 Århus C, Denmark
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18
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Pruitt SR, Nakata H, Nagata T, Mayes M, Alexeev Y, Fletcher G, Fedorov DG, Kitaura K, Gordon MS. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method. J Chem Theory Comput 2016; 12:1423-35. [DOI: 10.1021/acs.jctc.5b01208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Spencer R. Pruitt
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Hiroya Nakata
- Department of Fundamental Technology Research, R&D Center Kagoshima, Kyocera Corporation, 1-4 Kokubu Yamashita-cho, Kirishima-shi, Kagoshima 899-4312, Japan
| | - Takeshi Nagata
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Maricris Mayes
- Department
of Chemistry and Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, Dartmouth, Massachusetts 02747-2300, United States
| | - Yuri Alexeev
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Graham Fletcher
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass
Avenue, Lemont, Illinois 60439, United States
| | - Dmitri G. Fedorov
- Nanosystem Research
Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umenzono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, 201 Spedding
Hall, Ames, Iowa 50011, United States
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19
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Anacker T, Tew DP, Friedrich J. First UHF Implementation of the Incremental Scheme for Open-Shell Systems. J Chem Theory Comput 2015; 12:65-78. [PMID: 26605975 DOI: 10.1021/acs.jctc.5b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The incremental scheme makes it possible to compute CCSD(T) correlation energies to high accuracy for large systems. We present the first extension of this fully automated black-box approach to open-shell systems using an Unrestricted Hartree-Fock (UHF) wave function, extending the efficient domain-specific basis set approach to handle open-shell references. We test our approach on a set of organic and metal organic structures and molecular clusters and demonstrate standard deviations from canonical CCSD(T) values of only 1.35 kJ/mol using a triple ζ basis set. We find that the incremental scheme is significantly more cost-effective than the canonical implementation even for relatively small systems and that the ease of parallelization makes it possible to perform high-level calculations on large systems in a few hours on inexpensive computers. We show that the approximations that make our approach widely applicable are significantly smaller than both the basis set incompleteness error and the intrinsic error of the CCSD(T) method, and we further demonstrate that incremental energies can be reliably used in extrapolation schemes to obtain near complete basis set limit CCSD(T) reaction energies for large systems.
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Affiliation(s)
- Tony Anacker
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
| | - David P Tew
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Joachim Friedrich
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
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20
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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21
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Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method. J Chem Phys 2015; 142:124101. [DOI: 10.1063/1.4915068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Pruitt SR, Brorsen KR, Gordon MS. Ab initio investigation of the aqueous solvation of the nitrate ion. Phys Chem Chem Phys 2015; 17:27027-34. [DOI: 10.1039/c5cp04445f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The turning point between surface and interior solvation of NO3− is predicted to lie around a cluster size of (H2O)64.
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Affiliation(s)
- Spencer R. Pruitt
- Argonne Leadership Computing Facility
- Argonne
- USA
- Department of Chemistry
- Iowa State University
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23
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A Mini-review on Chemoinformatics Approaches for Drug Discovery. JOURNAL OF COMPUTER AIDED CHEMISTRY 2015. [DOI: 10.2751/jcac.16.15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Brorsen KR, Zahariev F, Nakata H, Fedorov DG, Gordon MS. Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:5297-307. [DOI: 10.1021/ct500808p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kurt R. Brorsen
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Federico Zahariev
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Kanagawa, Yokohama 226-8501, Japan
- Nakamura
Laboratory, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society
for the Promotion of Science, Kojimachi
Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- NRI, National
Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Mark S. Gordon
- Ames
Laboratory, U.S. Department of Energy (US-DOE), Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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25
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Pruitt SR, Bertoni C, Brorsen KR, Gordon MS. Efficient and accurate fragmentation methods. Acc Chem Res 2014; 47:2786-94. [PMID: 24810424 DOI: 10.1021/ar500097m] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.
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Affiliation(s)
- Spencer R. Pruitt
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, United States
| | - Colleen Bertoni
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kurt R. Brorsen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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26
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Riplinger C, Neese F. An efficient and near linear scaling pair natural orbital based local coupled cluster method. J Chem Phys 2013; 138:034106. [PMID: 23343267 DOI: 10.1063/1.4773581] [Citation(s) in RCA: 1100] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 10(5)-10(6) relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy estimate based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calculations reported here featured >8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.
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Affiliation(s)
- Christoph Riplinger
- Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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27
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Nakata H, Nagata T, Fedorov DG, Yokojima S, Kitaura K, Nakamura S. Analytic second derivatives of the energy in the fragment molecular orbital method. J Chem Phys 2013; 138:164103. [DOI: 10.1063/1.4800990] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Kristensen K, Kjærgaard T, Høyvik IM, Ettenhuber P, Jørgensen P, Jansik B, Reine S, Jakowski J. The divide–expand–consolidate MP2 scheme goes massively parallel. Mol Phys 2013. [DOI: 10.1080/00268976.2013.783941] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Kasper Kristensen
- a qLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
| | - Thomas Kjærgaard
- a qLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
| | - Ida-Marie Høyvik
- a qLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
| | - Patrick Ettenhuber
- a qLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
| | - Poul Jørgensen
- a qLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
| | - Branislav Jansik
- b IT4Innovations , VSB – Technical University of Ostrava , 17. listopadu 15/2172, Ostrava , Czech Republic
| | - Simen Reine
- c Centre for Theoretical and Computational Chemistry, Department of Chemistry , Oslo University , Postbox 1033, Blindern, 0315, Oslo , Norway
| | - Jacek Jakowski
- d National Institute for Computational Sciences , JICS-ORNL , One Bethel Valley Road, Bldg. 5100 ms 6173, Oak Ridge , Tennessee , 37831 , USA
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29
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Okamoto T, Ishikawa T, Koyano Y, Yamamoto N, Kuwata K, Nagaoka M. A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120216] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuya Okamoto
- Graduate School of Information Science, Nagoya University
| | - Takeshi Ishikawa
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
| | | | | | - Kazuo Kuwata
- Division of Prion Research, Center for Emerging Infectious Disease, Gifu University
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30
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Kobayashi M, Nakai H. An effective energy gradient expression for divide-and-conquer second-order Møller–Plesset perturbation theory. J Chem Phys 2013; 138:044102. [DOI: 10.1063/1.4776228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Kristensen K, Jørgensen P, Jansík B, Kjærgaard T, Reine S. Molecular gradient for second-order Møller-Plesset perturbation theory using the divide-expand-consolidate (DEC) scheme. J Chem Phys 2012; 137:114102. [DOI: 10.1063/1.4752432] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Nakata H, Fedorov DG, Nagata T, Yokojima S, Ogata K, Kitaura K, Nakamura S. Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient. J Chem Phys 2012; 137:044110. [DOI: 10.1063/1.4737860] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Steinmann C, Fedorov DG, Jensen JH. The effective fragment molecular orbital method for fragments connected by covalent bonds. PLoS One 2012; 7:e41117. [PMID: 22844433 PMCID: PMC3402534 DOI: 10.1371/journal.pone.0041117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.
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Affiliation(s)
- Casper Steinmann
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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34
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Nagata T, Fedorov DG, Li H, Kitaura K. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. J Chem Phys 2012; 136:204112. [DOI: 10.1063/1.4714601] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Tsukamoto T, Mochizuki Y, Watanabe N, Fukuzawa K, Nakano T. Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.03.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Ishikawa T, Kuwata K. RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital Method. J Phys Chem Lett 2012; 3:375-9. [PMID: 26285854 DOI: 10.1021/jz201697x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The second-order Møller-Plesset perturbation theory (MP2) gradient using resolution of the identity approximation (RI-MP2 gradient) was combined with the fragment molecular orbital (FMO) method to evaluate the gradient including electron correlation for large molecules. In this study, we adopted a direct implementation of the RI-MP2 gradient, in which a characteristic feature of the FMO scheme was utilized. Test calculations with a small peptide presented a computational advantage of the RI-MP2 gradient over the canonical MP2 gradient. In addition, it was shown that the error of the RI-MP2 gradient, caused by RI approximation, was negligible. As an illustrative example, we performed gradient calculations for two biomolecules-a prion protein with GN8 and a human immunodeficiency virus type 1 (HIV1) protease with lopinavir (LPV). These calculations demonstrated that the gradient including the correlation effect could be evaluated with only about twice the computational effort of the Hartree-Fock (HF) gradient.
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Affiliation(s)
- Takeshi Ishikawa
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuo Kuwata
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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38
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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39
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Kristensen K, Høyvik IM, Jansik B, Jørgensen P, Kjærgaard T, Reine S, Jakowski J. MP2 energy and density for large molecular systems with internal error control using the Divide-Expand-Consolidate scheme. Phys Chem Chem Phys 2012; 14:15706-14. [DOI: 10.1039/c2cp41958k] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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