NAMD goes quantum: An integrative suite for hybrid simulations

Marcelo C.R. Melo, Rafael C. Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C. Phillips, Julio D.C. Maia, Gerd B. Rocha, João V. Ribeiro, John E. Stone, Frank Neese, Klaus Schulten, Zaida Ann Luthey-Schulten

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)351-354
Number of pages4
JournalNature Methods
Volume15
Issue number5
DOIs
StatePublished - Apr 27 2018

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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