NAMD goes quantum: an integrative suite for hybrid simulations
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 visualizatio...
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ftpubman:oai:pure.mpg.de:item_2597548 2024-09-15T18:28:52+00:00 NAMD goes quantum: an integrative suite for hybrid simulations Melo, M. Bernardi, R. Rudack, T. Scheurer, M. Riplinger, C. Phillips, J. Maia, J. Rocha, G. Ribeiro, J. Stone, J. Neese, F. Schulten, K. Luthey-Schulten, Z. 2018-05-01 http://hdl.handle.net/21.11116/0000-0001-7EDB-C eng eng info:eu-repo/semantics/altIdentifier/doi/10.1038/nmeth.4638 http://hdl.handle.net/21.11116/0000-0001-7EDB-C Nature methods info:eu-repo/semantics/article 2018 ftpubman https://doi.org/10.1038/nmeth.4638 2024-07-31T09:31:29Z 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. Article in Journal/Newspaper Orca Max Planck Society: MPG.PuRe Nature Methods 15 5 351 354 |
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Max Planck Society: MPG.PuRe |
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English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Melo, M. Bernardi, R. Rudack, T. Scheurer, M. Riplinger, C. Phillips, J. Maia, J. Rocha, G. Ribeiro, J. Stone, J. Neese, F. Schulten, K. Luthey-Schulten, Z. |
spellingShingle |
Melo, M. Bernardi, R. Rudack, T. Scheurer, M. Riplinger, C. Phillips, J. Maia, J. Rocha, G. Ribeiro, J. Stone, J. Neese, F. Schulten, K. Luthey-Schulten, Z. NAMD goes quantum: an integrative suite for hybrid simulations |
author_facet |
Melo, M. Bernardi, R. Rudack, T. Scheurer, M. Riplinger, C. Phillips, J. Maia, J. Rocha, G. Ribeiro, J. Stone, J. Neese, F. Schulten, K. Luthey-Schulten, Z. |
author_sort |
Melo, M. |
title |
NAMD goes quantum: an integrative suite for hybrid simulations |
title_short |
NAMD goes quantum: an integrative suite for hybrid simulations |
title_full |
NAMD goes quantum: an integrative suite for hybrid simulations |
title_fullStr |
NAMD goes quantum: an integrative suite for hybrid simulations |
title_full_unstemmed |
NAMD goes quantum: an integrative suite for hybrid simulations |
title_sort |
namd goes quantum: an integrative suite for hybrid simulations |
publishDate |
2018 |
url |
http://hdl.handle.net/21.11116/0000-0001-7EDB-C |
genre |
Orca |
genre_facet |
Orca |
op_source |
Nature methods |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1038/nmeth.4638 http://hdl.handle.net/21.11116/0000-0001-7EDB-C |
op_doi |
https://doi.org/10.1038/nmeth.4638 |
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Nature Methods |
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15 |
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5 |
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351 |
op_container_end_page |
354 |
_version_ |
1810470298590380032 |