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The implementation of a fast and accurate QM/MM potential method in Amber
Author(s) -
Walker Ross C.,
Crowley Michael F.,
Case David A.
Publication year - 2008
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.20857
Subject(s) - qm/mm , mndo , periodic boundary conditions , molecular dynamics , computation , chemistry , computational science , computational chemistry , computer science , boundary value problem , physics , algorithm , molecule , quantum mechanics , organic chemistry
Version 9 of the Amber simulation programs includes a new semi‐empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi‐empirical Hamiltonians as well as the self‐consistent charge density functional tight binding (SCC‐DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008