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  NAMD goes quantum: an integrative suite for hybrid simulations

Melo, M. C. R., Bernardi, R. C., Rudack, T., Scheurer, M., Riplinger, C., Phillips, J. C., et al. (2018). NAMD goes quantum: an integrative suite for hybrid simulations. Nature methods, 15(5), 351-354. doi:10.1038/nmeth.4638.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0001-7EDB-C Version Permalink: https://hdl.handle.net/21.11116/0000-0001-7EDC-B
Genre: Journal Article

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 Creators:
Melo, Marcelo C. R.1, 2, Author
Bernardi, Rafael C.1, Author
Rudack, Till1, 3, Author
Scheurer, Maximilian4, 5, Author
Riplinger, Christoph6, Author
Phillips, James C.1, Author
Maia, Julio D. C.7, Author
Rocha, Gerd B.8, Author
Ribeiro, João V.1, Author
Stone, John E.1, Author
Neese, Frank9, Author           
Schulten, Klaus1, 10, Author
Luthey-Schulten, Zaida1, 2, 10, 11, Author
Affiliations:
1NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA, ou_persistent22              
2Center for Biophysics and Computational Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA, ou_persistent22              
3Department of Biophysics, Ruhr-University Bochum, Bochum, Germany, ou_persistent22              
4Biochemistry Center, Heidelberg University, Heidelberg, Germany, ou_persistent22              
5Interdisciplinary Center for Scientific Computing, Heidelberg, Germany, ou_persistent22              
6FAccTs GmbH, Köln, Germany, ou_persistent22              
7Center for Informatics, Federal University of Paraíba, João Pessoa, Brazil, ou_persistent22              
8Department of Chemistry, Federal University of Paraíba, João Pessoa, Brazil, ou_persistent22              
9Research Department Neese, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_2541710              
10Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA, ou_persistent22              
11Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA, ou_persistent22              

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Free keywords: Biocatalysis; Biophysical chemistry; Computational biophysics; Computational models; Software
 Abstract: Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can be applied to studies of reaction mechanisms in locations ranging from active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry packages ORCA and MOPAC, we created an integrated, comprehensive, customizable, and easy-to-use suite (http://www.ks.uiuc.edu/Research/qmmm). Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise.

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Language(s): eng - English
 Dates: 2017-06-282018-02-072018-05-01
 Publication Status: Published online
 Pages: 4
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/nmeth.4638
 Degree: -

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Title: Nature methods
  Other : Nature methods
Source Genre: Journal
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Publ. Info: New York, NY : Nature Pub. Group
Pages: - Volume / Issue: 15 (5) Sequence Number: - Start / End Page: 351 - 354 Identifier: ISSN: 1548-7091
CoNE: https://pure.mpg.de/cone/journals/resource/111088195279556