Benzene−Pyridine Interactions Predicted by the Effective Fragment Potential Method

Smith, Quentin Anthony; Gordon, Mark S.; Slipchenko, Lyudmila V.

doi:10.1021/jp201039b

Cited by 50 publications

(51 citation statements)

References 37 publications

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“…Although it is possible to systematically improve the minimum geometry estimate (e.g., by increasing the grid resolution or expanding the basis set used in generating the fragments), it is not deemed necessary here. The goal of the present research is to develop a scientific software component to access the EFP method rather than validating the method itself; the latter task has been addressed in numerous other workssee recent works of Smith et al 46,47 and references therein.…”

Section: Application Of Qm/efp Component: Indole−benzene Interactionsmentioning

confidence: 99%

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

Gaenko

Windus

Sosonkina

et al. 2012

J. Chem. Theory Comput.

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The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecular systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. ABSTRACT:The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecular systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.

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Section: Application Of Qm/efp Component: Indole−benzene Interactionsmentioning

confidence: 99%

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

Gaenko

Windus

Sosonkina

et al. 2012

J. Chem. Theory Comput.

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“…The effective fragment potential (EFP) method is a model potential for describing intermolecular interactions. Applications of the EFP method include modeling hydrogen bonding and van der Waals interactions in clusters and liquids of different compositions, such as water clusters and water solutions of alcohols and ions, complexes of benzene and benzene derivatives, and complexes of DNA base pairs . Available extensions allow using the EFP method in biological environment and polypeptides .…”

Section: Introductionmentioning

confidence: 99%

Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

Kaliman

Slipchenko

2014

J Comput Chem

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A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing algorithm that uses a master/slave model. The software shows excellent parallel scaling up to several hundreds of CPU-cores across multiple nodes. The code uses functions only from the well-established MPI-1 standard that simplifies portability of the library. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time- and length-scales.

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“…[16][17][18][19][20][21][22][23][24][25][26] Recently, a systematic benchmark study of EFP using a popular S22 dataset for noncovalent interactions has been published. [16][17][18][19][20][21][22][23][24][25][26] Recently, a systematic benchmark study of EFP using a popular S22 dataset for noncovalent interactions has been published.…”

Section: Introductionmentioning

confidence: 99%

Effective fragment potential method in Q‐CHEM: A guide for users and developers

et al. 2013

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A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree-Fock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a "fragment-only" feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP module's workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q-CHEM's auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user-defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described.

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Benzene−Pyridine Interactions Predicted by the Effective Fragment Potential Method

Cited by 50 publications

References 37 publications

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

Effective fragment potential method in Q‐CHEM: A guide for users and developers

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