The Molecular Workbench Software

The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der Waals potentials, Coulomb interactions, harmonic approximations to bonds, external fields, effective hydrophobic/hydrophilic forces, as well as boundaries and bond formation/breaking rules. Meso-scale objects and their interactions based on the Gay-Berne model are supported. The resulting ensembles can illustrate energy conservation, gas laws, pressure, phase transitions, chemical bonding, chemical reactions, Maxwell velocity distribution, osmosis, electrolysis, electrophoresis, liquid crystals, polymers, protein folding, molecular recognition, and more. Molecular Workbench also provides an authoring environment that can be used to easily create, visualize, annotate, contextualize, cross-link and distribute molecular dynamics models. Students can use the software to explore a vast range of preexisting models, or to develop models of their own.
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