SMD: visual steering of molecular dynamics for protein design

SMD, a system for interactively steering molecular dynamics calculations of protein molecules, includes computation, visualization, and communication components. Biochemists can "tug" molecules into different shapes by specifying external forces in the graphical interface, which are added to internal forces representing atomic bonds and nonbonded interactions. SMD provides a new tool for biochemists to use in exploring the structure of proposed designs, as well as in more general applications such as exploring the molecular dynamics model itself. Its primary use is in modeling single large biomolecules in a bath of water acting as the solvent.