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NAMD goes quantum: An integrative suite for QM/MM simulations
Applications of hybrid QM/MM methods range from reactions in active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD/VMD with the quantum chemistry packages ORCA, and MOPAC, we provide an integra...
| Autores principales: | , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2018
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095686/ https://www.ncbi.nlm.nih.gov/pubmed/29578535 http://dx.doi.org/10.1038/nmeth.4638 |
| _version_ | 1783347983417344000 |
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| author | Melo, Marcelo C. R. Bernardi, Rafael C. Rudack, Till Scheurer, Maximilian Riplinger, Christoph Phillips, James C. Maia, Julio D. C. Rocha, Gerd B. Ribeiro, João V. Stone, John E. Neese, Frank Schulten, Klaus Luthey-Schulten, Zaida |
| author_facet | Melo, Marcelo C. R. Bernardi, Rafael C. Rudack, Till Scheurer, Maximilian Riplinger, Christoph Phillips, James C. Maia, Julio D. C. Rocha, Gerd B. Ribeiro, João V. Stone, John E. Neese, Frank Schulten, Klaus Luthey-Schulten, Zaida |
| author_sort | Melo, Marcelo C. R. |
| collection | PubMed |
| description | Applications of hybrid QM/MM methods range from reactions in active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD/VMD with the quantum chemistry packages ORCA, and MOPAC, we provide an integrated, comprehensive, customizable, and easy-to-use suite. Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise. |
| format | Online Article Text |
| id | pubmed-6095686 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2018 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-60956862018-09-26 NAMD goes quantum: An integrative suite for QM/MM simulations Melo, Marcelo C. R. Bernardi, Rafael C. Rudack, Till Scheurer, Maximilian Riplinger, Christoph Phillips, James C. Maia, Julio D. C. Rocha, Gerd B. Ribeiro, João V. Stone, John E. Neese, Frank Schulten, Klaus Luthey-Schulten, Zaida Nat Methods Article Applications of hybrid QM/MM methods range from reactions in active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD/VMD with the quantum chemistry packages ORCA, and MOPAC, we provide an integrated, comprehensive, customizable, and easy-to-use suite. Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise. 2018-03-26 2018-05 /pmc/articles/PMC6095686/ /pubmed/29578535 http://dx.doi.org/10.1038/nmeth.4638 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
| spellingShingle | Article Melo, Marcelo C. R. Bernardi, Rafael C. Rudack, Till Scheurer, Maximilian Riplinger, Christoph Phillips, James C. Maia, Julio D. C. Rocha, Gerd B. Ribeiro, João V. Stone, John E. Neese, Frank Schulten, Klaus Luthey-Schulten, Zaida NAMD goes quantum: An integrative suite for QM/MM simulations |
| title | NAMD goes quantum: An integrative suite for QM/MM simulations |
| title_full | NAMD goes quantum: An integrative suite for QM/MM simulations |
| title_fullStr | NAMD goes quantum: An integrative suite for QM/MM simulations |
| title_full_unstemmed | NAMD goes quantum: An integrative suite for QM/MM simulations |
| title_short | NAMD goes quantum: An integrative suite for QM/MM simulations |
| title_sort | namd goes quantum: an integrative suite for qm/mm simulations |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095686/ https://www.ncbi.nlm.nih.gov/pubmed/29578535 http://dx.doi.org/10.1038/nmeth.4638 |
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