Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

Komeiji, Yuto; Mochizuki, Yuji; Nakano, Tatsuya; Mori, Hirotoshi

doi:10.5772/35247

Cited by 15 publications

(9 citation statements)

References 60 publications

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“…An alternative to this approach is to run full MD simulation of a chemical reaction using EFMO. This has already been done for many chemical reactions using FMO-MD [73][74][75] and can be done in future with EFMO.…”

Section: Discussionmentioning

confidence: 99%

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

2013

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We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol−1 for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

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Section: Discussionmentioning

confidence: 99%

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

2013

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“…We performed a series of FMO-MD simulations [36] for [Ln(H2O)64] 3+ droplet models, and obtained systematic RDF and ADF data. The level of calculations was FMO3-HF [45,46] in conjunction with the 4f in-core MCP technique [37].…”

Section: Discussionmentioning

confidence: 99%

“…The three-body fragment corrected HF (FMO3-HF) [45] was furthermore usable for FMO-MD in conjunction with the revised DF procedure in 2010 [46]. A review article on FMO-MD is freely available [36].…”

Section: Methodsmentioning

confidence: 99%

“…Duvail et al [24] performed a series of MM MD for all Ln(III) ions and found that there is a crossover change in dominant coordination from nine to eight between Tb and Dy. They also pointed out the existence of an intermediate bi- In this proceeding, we report a series of MD simulation based on the fragment molecular orbital (FMO) method [35], termed as FMO-MD [36], for the hydrated Ln(III) ions. Note that FMO-MD is of a fully QM scheme where the energy and forces are evaluated at each step.…”

Section: Introductionmentioning

confidence: 99%

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Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln(III) Ions

Fujiwara

Mori

Komeiji

et al. 2015

Proceedings of Computational Science Workshop 2014 (CSW2014)

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“…The droplet was confined within a sphere (radius = 9.0 Å ) by a harmonic restraint as described in Refs. [13,14,39,40]. The time step and temperature for the FMO-MD runs was set to 1 fs and 300 K, respectively.…”

Section: Computational Detailsmentioning

confidence: 99%

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Matsuda

Mori

2014

J Solution Chem

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Using fragment molecular orbital-molecular dynamics (FMO-MD) simulation at the FMO3-HF/6-31G(d,p) level, the hydration of a Ra 2? ion was theoretically investigated. The first peaks of the radial distribution function (RDF) for Ra-O and Ra-H lengths were predicted to be 2.85 and 3.45 Å with broad envelopes in the ranges of 2.5-3.5 and 2.8-4.3 Å , respectively. The broad peaks shows that the first hydration shell of Ra 2? is much more flexible than those in the other hydrated divalent alkaline earth metal ions, i.e., Ra 2? is a structure-breaking ion. The hydration number of Ra 2? was predicted to be 8.1. From the angular distribution function (ADF), it was clarified that the octa hydrated Ra 2? ion has a flexible square antiprism structure at room temperature.

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Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

Cited by 15 publications

References 60 publications

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln(III) Ions

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

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