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Beginning in theoretical physics, the method of MD gained popularity in material science and since the 1970s also in biochemistry and biophysics. It serves as an important tool in protein structure determination and refinement (see also crystallography, NMRNuclear magnetic resonance NMR is a physical phenomenon involving the interaction of atomic nuclei placed in an external magnetic field with an applied electromagnetic field oscillating at a particular frequency. Magnetic conditions within the material ar). The interaction between the objects is either described by a force fieldIn general physics, a force field is a vector field representing the gradient of a potential. The vectors that are the values of a force field are forces, and so measured in units of force such as newtons and pounds. In the context of molecular dynamics, (classical MD), a
quantum chemical modelQuantum chemistry is the application of quantum mechanics to problems in chemistry. The description of the electronic behavior of atoms and molecules as pertains to their reactivity is an application of quantum chemistry. Since quantum-mechanical studies, or a mix between the two.Popular software packages for MD simulation of biological molecules include: AMBERAMBER (an acronym for Assisted Model Building and Energy Refinement is a force field for molecular dynamics developed by Peter Kollman's group in the University of California, San Francisco. AMBER is also the name for the molecular dynamics simulation pac, CHARMMCHARMM Chemistry at HARvard Macromolecular Mechanics is a force field for molecular dynamics as well as the name for the molecular dynamics simulation package associated with this force field. The CHARMM Development Project involves a network of developer (and the commercial version CHARMm), GROMACSGROMACS Groningen Machine for Chemical Simulations is a molecular dynamics simulation package developed in the University of Groningen. It started out as a rewrite of the Fortran77-based GROMOS in the C programming language and has grown into a highly opt, GROMOSGROMOS is a force field for molecular dynamics developed at the University of Groningen and the ETH Zurich. GROMOS (currently GROMOS96 is also the name for the molecular dynamics simulation package associated with this force field. See also Gromacs Extern, and NAMD.