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...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Article
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
Descripción
Sumario: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.

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