Fragment molecular orbital method: an approximate computational method for large molecules

Kitaura, Kazuo; Ikeo, Eiji; Asada, Toshio; Nakano, Tatsuya; Uebayasi, Masami

doi:10.1016/s0009-2614(99)00874-x

Cited by 1,264 publications

(1,159 citation statements)

References 12 publications

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“…binding/molecule Cluster Monomer (16) The average binding energy for each cluster size is obtained by summing E binding/molecule and dividing by the number of isomers. The FIEFMO method outperforms the FMO2 method for all clusters and basis sets investigated.…”

Section: Resultsmentioning

confidence: 99%

Fully Integrated Effective Fragment Molecular Orbital Method

Pruitt

Steinmann

Jensen

et al. 2013

J. Chem. Theory Comput.

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In this work, the effective fragment potential (EFP) method is fully integrated (FI) into the fragment molecular orbital (FMO) method to produce an effective fragment molecular orbital (EFMO) method that is able to account for all of the fundamental types of both bonded and intermolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the method is tested and compared to both the standard FMO method as well as to fully ab initio methods. It is shown that the FIEFMO method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%. Disciplines Chemistry CommentsReprinted (adapted) ABSTRACT: In this work, the effective fragment potential (EFP) method is fully integrated (FI) into the fragment molecular orbital (FMO) method to produce an effective fragment molecular orbital (EFMO) method that is able to account for all of the fundamental types of both bonded and intermolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the method is tested and compared to both the standard FMO method as well as to fully ab initio methods. It is shown that the FIEFMO method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%. INTRODUCTIONModern computational chemistry methods strive to accurately model chemical systems using efficient computational algorithms. Unfortunately, it is difficult to reconcile both of these goals, since most methods that are widely viewed as the most accurate 1 also require the most computational effort. A very effective compromise is the application of fragmentation approaches to these computationally intensive methods. Many such fragmentation methods have been introduced in recent years, 2−8 with several showing the ability to accurately model large molecular systems. Methods such as the systematic molecular fragmentation (SMF) method, 9−11 molecular fractionation with conjugate caps (MFCC), 12 the molecular tailoring approach (MTA), 13 and the explicit polarization potential (X-Pol) 14,15 have all exhibited success in describing different chemical systems.One such method, the fragment molecular orbital (FMO) method, 16 has been extensively developed 17 since the original implementation by Kitaura et al. Based upon a many-body expansion of the energy, the FMO method takes the effects of the entire system into account during each step of a given calculation through the use of an electrostatic potential (ESP). The FMO method, as well as other fragmentation methods, 18 also benefit from the relative ease with which calculations can be parallelized on modern computer architectures. This inherent parallelizability aids in lowering the computational cost of the most accurate ab initio methods.While not a fragmentation method in the same vein as the FMO method, the effective fragment potential (EFP) method 19−21 wa...

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Section: Resultsmentioning

confidence: 99%

Fully Integrated Effective Fragment Molecular Orbital Method

Pruitt

Steinmann

Jensen

et al. 2013

J. Chem. Theory Comput.

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“…Filling the gap, we propose such analysis based upon the fragment molecular orbital (FMO) method, 15,16 which prescribes the division of molecules into fragments and leads to ab initio calculations of fragments, their dimers and, optionally, trimers. Quantum mechanical calculations of very large systems [17][18][19][20] become possible: Ikegami et al 21 applied the FMO method to the study of the photosynthetic reaction center of Rhodopseudomonas viridis consisting of more than 20,000 atoms.…”

Section: Introductionmentioning

confidence: 99%

Pair interaction energy decomposition analysis

2006

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Abstract:The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H 2 O) 1024 , the helix, turn, and strand of polyalanine (ALA) 10 , as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.

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“…1,2 One strategy is to use a fragmentation approach, in which a large system of interest is divided into smaller subsystems, and ab initio calculations are performed on these smaller subsystems. 2 One of the most successful and extensively developed fragmentation methods is the fragment molecular orbital (FMO) method 3 proposed by Kitaura et al in 1999. The FMO method has been implemented for most ab initio and density functional theory (DFT) methods.…”

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confidence: 99%

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Brorsen

Minezawa

et al. 2012

J. Chem. Theory Comput.

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Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully analytic energy gradient results in better energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic energy gradient and two body corrections (FMO2) gives improved energy conservation compared with a previously calculated FMO-MD simulation with an approximate energy gradient and including up to three body corrections (FMO3). Disciplines Chemistry CommentsReprinted (adapted) ABSTRACT: Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully analytic energy gradient results in better energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic energy gradient and two body corrections (FMO2) gives improved energy conservation compared with a previously calculated FMO-MD simulation with an approximate energy gradient and including up to three body corrections (FMO3). INTRODUCTION1.1. Fragment Molecular Orbital Method. Much progress has been made recently in improving algorithms for ab initio calculations on large systems. 1,2 One strategy is to use a fragmentation approach, in which a large system of interest is divided into smaller subsystems, and ab initio calculations are performed on these smaller subsystems. 2 One of the most successful and extensively developed fragmentation methods is the fragment molecular orbital (FMO) method 3 proposed by Kitaura et al. in 1999. The FMO method has been implemented for most ab initio and density functional theory (DFT) methods. 4−8 Numerous approximations to the original FMO method have been implemented to improve the efficiency of the calculation. The two most important of these approximations are the electrostatic point charge (ESP-PC) approximation and the electrostatic dimer (ES-DIM) approximation. 9 The ESP-PC approximation calculates the FMO embedded electrostatic potential using point charges rather than two electron integrals, while the ES-DIM approximation calculates the dimer energy of two fragments using point charges rather than using ab initio methods.FMO gradients were developed soon after the introduction of the FMO method. 10 Improvements to the gradient followed that allowed the use of gradients with the ESP-PC approximation 11 and the ES-DIM approximation. 12 Because the dimer (or trimer) density is not iterated to self-consi...

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Fragment molecular orbital method: an approximate computational method for large molecules

Cited by 1,264 publications

References 12 publications

Fully Integrated Effective Fragment Molecular Orbital Method

Fully Integrated Effective Fragment Molecular Orbital Method

Pair interaction energy decomposition analysis

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

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