Literature DB >> 32321259

Recent developments in the general atomic and molecular electronic structure system.

Giuseppe M J Barca1, Colleen Bertoni2, Laura Carrington3, Dipayan Datta4, Nuwan De Silva5, J Emiliano Deustua6, Dmitri G Fedorov7, Jeffrey R Gour8, Anastasia O Gunina4, Emilie Guidez9, Taylor Harville4, Stephan Irle10, Joe Ivanic11, Karol Kowalski12, Sarom S Leang3, Hui Li13, Wei Li14, Jesse J Lutz15, Ilias Magoulas6, Joani Mato4, Vladimir Mironov16, Hiroya Nakata17, Buu Q Pham4, Piotr Piecuch6, David Poole4, Spencer R Pruitt4, Alistair P Rendell1, Luke B Roskop18, Klaus Ruedenberg4, Tosaporn Sattasathuchana4, Michael W Schmidt4, Jun Shen6, Lyudmila Slipchenko19, Masha Sosonkina20, Vaibhav Sundriyal20, Ananta Tiwari3, Jorge L Galvez Vallejo4, Bryce Westheimer4, Marta Włoch21, Peng Xu4, Federico Zahariev4, Mark S Gordon4.   

Abstract

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Year:  2020        PMID: 32321259     DOI: 10.1063/5.0005188

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  48 in total

1.  Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory.

Authors:  Felix N Tomilin; Anastasia V Rogova; Ludmila P Burakova; Olga N Tchaikovskaya; Pavel V Avramov; Dmitri G Fedorov; Eugene S Vysotski
Journal:  Photochem Photobiol Sci       Date:  2021-04-08       Impact factor: 3.982

2.  SN2 versus E2 reactions in a complex microsolvated environment: theoretical analysis of the equilibrium and activation steps of a nucleophilic fluorination.

Authors:  Fernando M Lisboa; Josefredo R Pliego
Journal:  J Mol Model       Date:  2022-05-21       Impact factor: 1.810

3.  Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Authors:  Daniel G A Smith; Annabelle T Lolinco; Zachary L Glick; Jiyoung Lee; Asem Alenaizan; Taylor A Barnes; Carlos H Borca; Roberto Di Remigio; David L Dotson; Sebastian Ehlert; Alexander G Heide; Michael F Herbst; Jan Hermann; Colton B Hicks; Joshua T Horton; Adrian G Hurtado; Peter Kraus; Holger Kruse; Sebastian J R Lee; Jonathon P Misiewicz; Levi N Naden; Farhad Ramezanghorbani; Maximilian Scheurer; Jeffrey B Schriber; Andrew C Simmonett; Johannes Steinmetzer; Jeffrey R Wagner; Logan Ward; Matthew Welborn; Doaa Altarawy; Jamshed Anwar; John D Chodera; Andreas Dreuw; Heather J Kulik; Fang Liu; Todd J Martínez; Devin A Matthews; Henry F Schaefer; Jiří Šponer; Justin M Turney; Lee-Ping Wang; Nuwan De Silva; Rollin A King; John F Stanton; Mark S Gordon; Theresa L Windus; C David Sherrill; Lori A Burns
Journal:  J Chem Phys       Date:  2021-11-28       Impact factor: 3.488

4.  Expanding the known structure space for RNA binding: a test of 2,5-diketopiperazine.

Authors:  Diego M Arévalo; Viktoriya S Anokhina; Oliver L R Swart; Benjamin L Miller
Journal:  Org Biomol Chem       Date:  2022-01-19       Impact factor: 3.876

5.  Molecular docking study and antireabsorptive activity of a semi-synthetic coumarin derivative from Platymiscium floribundum in the ligature-induced periodontitis in rats: the involvement of heme oxygenase-1.

Authors:  Ana Larissa de Q França; Hellíada V Chaves; Jordânia M de O Freire; Luzia Hermínia T de Sousa; Antônia T A Pimenta; Mary Anne S Lima; Bruna R de Oliveira; Marcos Carlos de Mattos; Vicente de Paulo T Pinto; Antônia Moêmia L R Portela; Karuza Maria A Pereira; José Jackson do N Costa; Paula Goes; Roberta Jeane B Jorge; João Alison de M Silveira; Helyson Lucas B Braz; Maria Elisabete A de Moraes; Mirna M Bezerra
Journal:  Clin Oral Investig       Date:  2021-08-19       Impact factor: 3.573

6.  Isoenergetic two-photon excitation enhances solvent-to-solute excited-state proton transfer.

Authors:  Jurick Lahiri; Mehdi Moemeni; Jessica Kline; Ilias Magoulas; Stephen H Yuwono; Maryann Laboe; Jun Shen; Babak Borhan; Piotr Piecuch; James E Jackson; G J Blanchard; Marcos Dantus
Journal:  J Chem Phys       Date:  2020-12-14       Impact factor: 3.488

7.  Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.

Authors:  Raju Sarkar; Akhilesh Jaiswar; Scott P Hennelly; José N Onuchic; Karissa Y Sanbonmatsu; Susmita Roy
Journal:  J Phys Chem B       Date:  2021-06-09       Impact factor: 2.991

8.  Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.

Authors:  Peng Xu; Tosaporn Sattasathuchana; Emilie Guidez; Simon P Webb; Kilinoelani Montgomery; Hussna Yasini; Iara F M Pedreira; Mark S Gordon
Journal:  J Chem Phys       Date:  2021-03-14       Impact factor: 3.488

9.  Computational Resources for Bioscience Education.

Authors:  Rajiv K Kar
Journal:  Appl Biochem Biotechnol       Date:  2021-06-08       Impact factor: 2.926

10.  Density-functional tight-binding for phosphine-stabilized nanoscale gold clusters.

Authors:  Van Quan Vuong; Jenica Marie L Madridejos; Bálint Aradi; Bobby G Sumpter; Gregory F Metha; Stephan Irle
Journal:  Chem Sci       Date:  2020-11-02       Impact factor: 9.825

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