Literature DB >> 26623658

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

Yoshio Nishimoto1,2, Hiroya Nakata3,4, Dmitri G Fedorov5, Stephan Irle1,6.   

Abstract

The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.

Entities:  

Year:  2015        PMID: 26623658     DOI: 10.1021/acs.jpclett.5b02490

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  2 in total

1.  Identification of Novel Natural Product Inhibitors against Matrix Metalloproteinase 9 Using Quantum Mechanical Fragment Molecular Orbital-Based Virtual Screening Methods.

Authors:  Hocheol Lim; Hansol Hong; Seonik Hwang; Song Ja Kim; Sung Yum Seo; Kyoung Tai No
Journal:  Int J Mol Sci       Date:  2022-04-18       Impact factor: 6.208

2.  Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

Authors:  Mikhail A Hameedi; Erica T Prates; Michael R Garvin; Irimpan I Mathews; B Kirtley Amos; Omar Demerdash; Mark Bechthold; Mamta Iyer; Simin Rahighi; Daniel W Kneller; Andrey Kovalevsky; Stephan Irle; Van-Quan Vuong; Julie C Mitchell; Audrey Labbe; Stephanie Galanie; Soichi Wakatsuki; Daniel Jacobson
Journal:  Nat Commun       Date:  2022-09-08       Impact factor: 17.694

  2 in total

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