Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods<sup>†</sup>

Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

doi:10.1021/jp101498m

Cited by 80 publications

(102 citation statements)

References 44 publications

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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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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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“…37,38 The original EFMO method uses the fragmentation scheme from the FMO method and treats the separated fragment interactions using the Coulomb interaction of the EFP method. Additionally, the ESP used during standard FMO calculations is replaced with the many-body polarization of the EFP method.…”

Section: Introductionmentioning

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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“…To calculate the fully analytic Hessian, one must solve the CPHF equations, and the SCZV procedure would play an essential role. The SCZV procedure could also be found useful in other fragmentation methods that require the response term (some methods 87,96 do not need it with respect to the field, although the Mulliken charge derivatives do require it 97,80 ).…”

Section: Discussionmentioning

confidence: 99%

Fully analytic energy gradient in the fragment molecular orbital method

Brorsen¹,

Fedorov²

2011

The Journal of Chemical Physics

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The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H 2 O) 64 , alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO selfconsistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes. KeywordsPolymers, Electrostatics, Chemical bonds, Proteins, Density functional theory Disciplines Chemistry CommentsThe following article appeared in Journal of Chemical Physics 134 (2011) The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H 2 O) 64 , alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO self-consistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes.

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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods^†

Cited by 80 publications

References 44 publications

The Melting Temperature of Liquid Water with the Effective Fragment Potential

The Melting Temperature of Liquid Water with the Effective Fragment Potential

Fully Integrated Effective Fragment Molecular Orbital Method

Fully analytic energy gradient in the fragment molecular orbital method

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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods†

Cited by 80 publications

References 44 publications

The Melting Temperature of Liquid Water with the Effective Fragment Potential

The Melting Temperature of Liquid Water with the Effective Fragment Potential

Fully Integrated Effective Fragment Molecular Orbital Method

Fully analytic energy gradient in the fragment molecular orbital method

Contact Info

Product

Resources

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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods^†