Molecular dynamics jobs simulate the Newtonian dynamics of the model system, producing a trajectory of the particles, coordinates, velocities, and energies, on which statistical analysis can be performed to derive properties of interest about the model system. The molecular dynamics task performs a single MD simulation under the chosen ensemble condition for a given model system, generating simulation data for post-simulation analysis. The Molecular Dynamics panel is designed to make setting up jobs as easy as possible. The main panel provides the most common simulation controls, while the Advanced Options dialog box provides access to a larger range of parameters. The default values represent a good balance between accuracy and performance and work for most jobs without change, but can be changed as needed.
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