The implementation of a fast and accurate QM/MM potential method in Amber

Content Provider	Semantic Scholar
Author	Walker, Ross C. Crowley, Michael F. Case, David A.
Copyright Year	2008
Abstract	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.
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Alternate Webpage(s)	https://www.researchgate.net/profile/Michael_Crowley5/publication/5776561_The_implementation_of_a_fast_and_accurate_QMMM_potential_method_in_Amber/links/02bfe50f586af76277000000.pdf
Alternate Webpage(s)	http://www.mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/ReadingMaterials/JCompChem_2008_29_1019-1031_Amber_QMMM_Paper.pdf
Alternate Webpage(s)	https://www.wikidata.org/entity/Q46159606
PubMed reference number	18072177v1
Alternate Webpage(s)	https://doi.org/10.1002/jcc.20857
DOI	10.1002/jcc.20857
Journal	Journal of Computational Chemistry
Volume Number	29
Issue Number	7
Language	English
Access Restriction	Open
Subject Keyword	Approximation Assisted Model Building with Energy Refinement (AMBER) Atom Austin Model 1 CHARMM Central processing unit Code Computation Density functional theory Ewald summation Force field (chemistry) Gradient Implicit solvation Intracisternal A-Particle Elements Less Than MNDO Molecular dynamics PM3 (chemistry) Particle Mesh Potential method Preparation QM/MM Rewrite (programming) Semiconductor industry Series acceleration Simulation Thermostat Device Component Tight binding User Interface Device Component Water model
Content Type	Text
Resource Type	Article