CHARMM chemistry at Harvard

CHARMM (chemistry at Harvard macromolecular mechanics) a molecular mechanics force field... 

Note The BIO+ force field is an implementation of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field developed in the group of Martin Karplus at Harvard University. Like AMBER and OPLS, it is primarily designed to explore macromolecules. 

CHARMM (Chemistry at HARvard Molecular Mechanics) General-purpose... 

The GEMM software on the ST-100 is not a stand-alone package, and it requires a front-end simulation software package that runs on the host to provide data and to send command requests. It was designed and written with CHARMM (Chemistry at HARvard Macro-molecular Mechanics) (14) as the primary front-end, but additional software packages, such as AMBER (15), have subsequently been modified to drive GEMM. 

The CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field is designed for the modelling (both molecular mechanics and dynamics calculations) of macromolecular systems [67]. A revision for carbohydrates was made by Ha et al. [40]. Kouwijzer and Grootenhuis [68-69] redeveloped the CHEAT force field a CHARMm-based force field for carbohydrates with which a molecule in aqueous solution is mimicked by a simulation of the isolated molecule. 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

Brooks BR et al (2009) CHARMM - Chemistry at HARvard Macromolecular Mechanics (22 and higher) available at http /Avww.charmm.org... 

CHARMM = Chemistry at Harvard Macromolecular Mechanics MMFF = Merck molecular force field QM = quantum mechanics. 

AMBER = assisted model building with energy refinement force field CHARMM = chemistry at Harvard macromolecu-lar mechanics force field MP4SDQ = Mpller-Plesset fourth-order perturbation theory with corrections for single, double, and quadruple excitations OPLS = optimized potentials for liquid simulation force field TZP = triple-zeta -f polarization. 

The CHARMM (Chemistry at Harvard macromolecular mechanics) force field has been developed in the laboratory of Karplus (see CHARMM The Energy Function and Its Parameterization). The first, 1983, version was designed as a united type force field for protein and nucleic acids, where hydrogens of the CH3, CH2, and CH groups were treated implicitly. This approximation was important in protein modeling, but is inessential in the case of nucleic acid calculations. An improved all-atom model, specifically designed for the nucleic acids has been presented in 1986. Recently, in 1995, another reparametrized version of the CHARMM nucleic acid force field has been published. ... 

CHARMm Chemistry at Harvard molecular mechanics. (Ref. 17) Optimized for proteins and DNA. Depends on system but generally good. 

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