Chemistry at Harvard molecular mechanics

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

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. 

The rhodopsin protein problem An all-atom rhodopsin protein was set in a solvated lipid bilayer described via the Chemistry at Harvard Molecular Mechanics (CHARMM) force field. Long-range coulomb interactions were described via the particle-particle mesh. SHAKE constraints were applied to the system for the definitions of the force field and constraints. Further, the model consisted of counter ions with a reduced amount of water the effect was to have a total system with 32,000 atoms that was simulated for 100 time steps. This simulation was performed at a constant pressure and temperature with an LJ force cutoff of 10.0 Angstroms. In this problem, the total number of neighbors per atom was 440 within this force cutoff More information about the benchmark problem can be found at http //lammps.sandia.gOv/bench.html rhodo... 

CHARMM, which stands for Chemistry at HARvard Molecular Mechanics, is one of the oldest and most widely used MD codes. It originated... 

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

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

Tel. 617-495-4018, fax 617-495-1792, e-mail karplus huchel.bitnet Molecular dynamics package using Chemistry at Harvard Macromolecular Mechanics force field. Extensive scripting language for molecular mechanics, simulations, solvation, electrostatics, crystal packing, vibrational analysis, free energy perturbation (FEP) calculations, quantum mechanics/molecular mechanics calculations, stochastic dynamics, and graphing data. 

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. 

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

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. 

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

---