Dynamics

Easily Investigate and Visualize Molecular Structure and Mobility

Overview

Molecular dynamics allows scientists to simulate molecular motion, explore conformational space, and gain insight into molecular structure and mobility. Molecular dynamics can generate an ensemble of conformers for a particular structure, or follow the evolution of a system over time. Molecular dynamics has been shown to be more efficient than Monte Carlo methods for simulation of complex molecules. Dynamics™ provides a number of techniques for producing such ensembles, as well as the graphical tools required for organizing and analyzing the resulting structures. Dynamics' flexible setup, visualization, and statistical analysis tools make it a valuable addition to the SYBYL^® expert molecular modeling environment.

Dynamics Brochure (736k)

Dynamics simulation of ethidium intercalation into a double-stranded DNA molecule with Na+ counterions using the AMBER7 FF99 force field in SYBYL. As the simulation progresses, the position of ethidium changes from its initial placement in the major groove to its intercalation and stacking between two adjacent base-pairs. A separation of the base-pairs is observed as well as a kink in the pseudo-dyad axis. This simulation included explicit solvent in the form of water molecules (present, but undisplayed for clarity). (From an experimental study designed by Dr. Regina Monaco, Div. Env. Hlth. Sci., MSPH, Columbia University, New York.)
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Key Benefits

Intuitive graphical interface for setup and results analysis
User control of simulation parameters
Extensive documentation, including detailed theory description and tips for better calculations
Multiple options for solvent treatment
Multiple methods of simulated annealing
Tight integration with the Molecular Spreadsheet^™ for easy, detailed analysis

Radius of Gyration creates a "chrysanthemum" - a fatty acid is tethered at the carboxylate end of the molecule and followed for 50 picoseconds in a Dynamics run. The molecule is color-coded by the amount of local translation of the atoms.

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