Fully Integrated Effective Fragment Molecular Orbital Method

Pruitt, Spencer R.; Steinmann, Casper; Jensen, Jan H.; Gordon, Mark S.

doi:10.1021/ct4001119

Cited by 55 publications

(64 citation statements)

References 65 publications

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“…Response terms are now included in the FMO gradient for RHF, UHF, MP2, and DFT, and a future promising research direction will be to extend the analytic gradient to other FMO methods, such as multilayer FMO, 47 three-body FMO, 48 FMO with an auxiliary basis set, 49 and the effective fragment molecular orbital method. 50 …”

Section: Discussionmentioning

confidence: 99%

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Brorsen

Zahariev

Nakata

et al. 2014

J. Chem. Theory Comput.

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The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories. Disciplines Chemistry CommentsReprinted ( ABSTRACT: The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO−DFT gradient, which lacks response terms, the FMO−DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO−DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn− Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO−DFT is a nonvariational method and the FMO−DFT gradient is unique compared to standard DFT gradients in that the FMO−DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories.

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Section: Discussionmentioning

confidence: 99%

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Brorsen

Zahariev

Nakata

et al. 2014

J. Chem. Theory Comput.

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“…61 Issues related to the rigid monomer geometry and its influence on the estimate of T m will be addressed in future studies using the effective fragment molecular orbital (EFMO) method, 62,63 which is based on flexible fragments. It is possible that the EFP method is …”

Section: The Journal Of Physical Chemistry Lettersmentioning

confidence: 99%

The Melting Temperature of Liquid Water with the Effective Fragment Potential

Brorsen

Willow

Xantheas

et al. 2015

J. Phys. Chem. Lett.

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The direct simulation of the solid-liquid water interface with the effective fragment potential (EFP) via the constant enthalpy and pressure (NPH) ensemble was used to estimate the melting temperature (Tm) of iceIh. Initial configurations and velocities, taken from equilibrated constant pressure and temperature (NPT) simulations at P = 1 atm and T = 305 K, 325 K and 399 K, respectively, yielded corresponding Tm values of 378 ± 16 K, 382 ± 14 K and 384 ± 15 K. These estimates are consistently higher than experiment, albeit to the same degree as previously reported estimates using density functional theory (DFT)-based Born-Oppenheimer simulations with the Becke-Lee-Yang-Parr functional plus dispersion corrections (BLYP-D). C

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“…For modeling intermolecular interactions, similar strategies based on multipolar expansion have been utilized. [39][40][41] Recently, EFP was combined with fragment molecular orbital (FMO) method 42 giving rise to the EFMO method capable of describing both molecular aggregates and large molecules 43,44 (however, EFMO method has not yet been extended to excited states). Detailed reviews of various flavors of fragment-based methods can be found in Refs.…”

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confidence: 99%

Extension of the Effective Fragment Potential Method to Macromolecules

et al. 2016

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The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

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Fully Integrated Effective Fragment Molecular Orbital Method

Cited by 55 publications

References 65 publications

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

The Melting Temperature of Liquid Water with the Effective Fragment Potential

Extension of the Effective Fragment Potential Method to Macromolecules

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