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The QM‐MM interface for CHARMM‐deMon
Author(s) -
Lev Bogdan,
Zhang Rui,
de la Lande Aurélien,
Salahub Dennis,
Noskov Sergei Yu
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21387
Subject(s) - integrator , molecular dynamics , force field (fiction) , qm/mm , thermostat , hamiltonian (control theory) , statistical physics , minification , energy minimization , computational science , computer science , chemistry , physics , computational chemistry , thermodynamics , mathematical optimization , quantum mechanics , mathematics , voltage , programming language
We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi‐particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force‐field (CHARMM27) or a polarizable force‐field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual‐thermostat method and the VV2 integrator to run molecular dynamics simulations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010