Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 29, Issue 7, Pages 1019-1031Publisher
WILEY
DOI: 10.1002/jcc.20857
Keywords
molecular dynamics; Amber; QM/MM; quantum mechanics; MD; PME; particle mesh Ewald; Ewald; molecular mechanics
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Funding
- NIGMS NIH HHS [GM57513] Funding Source: Medline
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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 MID 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. (C) 2007 Wiley Periodicals, Inc.
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