NAMD goes quantum: an integrative suite for hybrid simulations

Nat Methods. 2018 May;15(5):351-354. doi: 10.1038/nmeth.4638. Epub 2018 Mar 26.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation*
  • Models, Biological*
  • Models, Chemical*
  • Molecular Dynamics Simulation
  • Quantum Theory*
  • Software*
  • Static Electricity