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Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to ...
GROMOS (GROningen MOlecular Simulation) – a force field that comes as part of the GROMOS software, a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. [72] GROMOS force field A-version has been developed for application to aqueous or apolar solutions of proteins, nucleotides, and sugars.
The simplest approach to satisfying constraints in energy minimization and molecular dynamics is to represent the mechanical system in so-called internal coordinates corresponding to unconstrained independent degrees of freedom of the system. For example, the dihedral angles of a protein are an independent set of coordinates that specify the ...
The Morse potential has been applied to studies of molecular vibrations and solids, [22] and also inspired the functional form of more accurate potentials such as the bond-order potentials. Ionic materials are often described by a sum of a short-range repulsive term, such as the Buckingham pair potential , and a long-range Coulomb potential ...
Coarse-grained models have found practical applications in molecular dynamics simulations. [1] Another case of interest is the simplification of a given discrete-state system, as very often descriptions of the same system at different levels of detail are possible.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
In chemistry and molecular physics, fluxional (or non-rigid) molecules are molecules that undergo dynamics such that some or all of their atoms interchange between symmetry-equivalent positions. [1] Because virtually all molecules are fluxional in some respects, e.g. bond rotations in most organic compounds , the term fluxional depends on the ...