Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein–Ligand Binding

Fedorov, Dmitri G.; Kitaura, Kazuo

doi:10.1002/9781119129271.ch3

Cited by 12 publications

(9 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To make input files, one can use graphical user interfaces: Facio 48 and FU. 73 Plots of pair interactions and visualization of the geometry of interacting fragments can be helpful in gaining insight into binding. A limited FMO support is available in software package MOE via SVL scripts 74 and in MacMolPlt.…”

Section: Fmo Methodology Fmo Basicsmentioning

confidence: 99%

See 1 more Smart Citation

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Fedorov

2017

WIREs Comput Mol Sci

Self Cite

120

122

View full text Add to dashboard Cite

The physical picture of the fragment molecular orbital (FMO) method is described on the basis of a many‐body expansion with terms describing the polarization of isolated fragments, charge transfer (CT), and exchange‐repulsion (EX) between them. Aspects of fragmentation are discussed in detail and FMO development in GAMESS‐US is summarized. Recent progress in method development and applications is reviewed, with a focus on studies of protein–ligand binding, excited states, and spectra of large molecular systems. WIREs Comput Mol Sci 2017, 7:e1322. doi: 10.1002/wcms.1322 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Ab Initio Electronic Structure Methods

show abstract

Section: Fmo Methodology Fmo Basicsmentioning

confidence: 99%

“…To make input files, one can use graphical user interfaces: Facio and FU . Plots of pair interactions and visualization of the geometry of interacting fragments can be helpful in gaining insight into binding.…”

Section: Fmo Methodologymentioning

confidence: 99%

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Fedorov

2017

WIREs Comput Mol Sci

Self Cite

120

122

View full text Add to dashboard Cite

show abstract

“…A water droplet (H 2 O) 1196 was generated using FU software. For the cc‐pVDZ basis set, ESP‐PC and ES‐DIM approximations were used with the default values of dimensionless thresholds (2.0); for the aug‐cc‐pVTZ basis set, the values were −1 and 4.0, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…In addition to PCM, the same algorithm developed in this work can be used for solvation model density (SMD) method interfaced with FMO [77] because SMD shares the electrostatic model with PCM and the main time-consuming work in both PCM and SMD is related to electrostatics. 1196 was generated using FU [78] software. For the cc-pVDZ basis set, ESP-PC and ES-DIM approximations were used with the default values of dimensionless thresholds (2.0); for the aug-cc-pVTZ basis set, the values were −1 and 4.0, respectively.…”

Section: Solvent Modelsmentioning

confidence: 99%

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

Mironov

Alexeev

Fedorov

2019

Int J of Quantum Chemistry

Self Cite

View full text Add to dashboard Cite

The fragment molecular orbital method in GAMESS is parallelized in a multithreaded OpenMP implementation combined with the MPI version of the two‐level generalized distributed data interface. The energy and analytic gradient in gas phase and the polarizable continuum model of solvation are parallelized in this hybrid three‐level scheme, achieving a large memory footprint reduction and a high parallel efficiency on Intel Xeon Phi processors. The parallel efficiency is demonstrated on the Stampede2 and Theta supercomputers using up to 2048 nodes (262 144 threads).

show abstract

“…For the FMO method, it is particularly important to have tools which can sensibly partition a system into fragments. The FU program 94 is one such tool, providing a GUI application that can be used to prepare crystal structure files, fix structure errors, create input files for FMO calculations, and visualize the results. FU is a python program with the ability to run arbitrary, user‐defined python scripts, which anticipates the complex workflows that may be required.…”

Section: Fragmentation Of Large Systemsmentioning

confidence: 99%

Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity

Dawson

Degomme

Stella

et al. 2021

WIREs Comput Mol Sci

View full text Add to dashboard Cite

In the past decade, developments of computational technology around density functional theory (DFT) calculations have considerably increased the system sizes which can be practically simulated. The advent of robust high performance computing algorithms which scale linearly with system size has unlocked numerous opportunities for researchers. This fact enables computational physicists and chemists to investigate systems of sizes which are comparable to systems routinely considered by experimentalists, leading to collaborations with a wide range of techniques and communities. This has important consequences for the investigation paradigms which should be applied to reduce the intrinsic complexity of quantum mechanical calculations of many thousand atoms. It becomes important to consider portions of the full system in the analysis, which have to be identified, analyzed, and employed as building‐blocks from which decomposed physico‐chemical observables can be derived. After introducing the state‐of‐the‐art in the large scale DFT community, we will illustrate the emerging research practices in this rapidly expanding field, and the knowledge gaps which need to be bridged to face the stimulating challenge of the simulation of increasingly realistic systems. This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Simulation Methods Structure and Mechanism > Computational Materials Science

show abstract

Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein–Ligand Binding

Cited by 12 publications

References 35 publications

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity

Contact Info

Product

Resources

About