NAMD goes quantum: an integrative suite for hybrid 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

doi:10.1038/nmeth.4638

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NAMD goes quantum: an integrative suite for hybrid simulations

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Neese, Frank
Research Department Neese, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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引用

Melo, M. C. R., Bernardi, R. C., Rudack, T., Scheurer, M., Riplinger, C., Phillips, J. C., Maia, J. D. C., Rocha, G. B., Ribeiro, J. V., Stone, J. E., Neese, F., Schulten, K., & Luthey-Schulten, Z. (2018). NAMD goes quantum: an integrative suite for hybrid simulations. Nature methods, 15(5), 351-354. doi:10.1038/nmeth.4638.

引用: https://hdl.handle.net/21.11116/0000-0001-7EDB-C

要旨

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.