TCB Publications - Abstract

Marcelo Melo, Rafael Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James Phillips, Julio Maia, Gerd Rocha, J. Ribeiro, John Stone, Frank Nesse, Klaus Schulten, and Zaida Luthey-Schulten. NAMD goes quantum: An integrative suite for QM/MM simulations. Nature Methods, 15:351-354, 2018. (PMC: PMC6095686)

MELO2018 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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