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This manual gives you a walk-through on how to use the Molecular Dynamics Plugin:



The Molecular Dynamics Plugin calculates the trajectory of a molecular system by integrating the equations of Newton's laws of motion. The generated trajectory can be visualized as a continuous animation or as a sequence of discrete frames.


Fig. 1 Trajectory of an MD run, shown as a sequence of frames




The following options can be set in the Molecular Dynamics Options panel:

  • Display: display mode
    • Animation: trajectory is displayed as an animation.
    • Frames: trajectory frames are displayed individually (see above).
  • Force field: force field used for calculation.
  • Integrator: integrator type used for solving the equations of Newton's laws of motion.
  • Simulation steps: number of simulation steps.
  • Step time (fs): time between simulation steps in femtoseconds.
  • Initial temperature (K): initial temperature of the system in kelvin.
  • Start time of display (fs): the time of the first simulation frame to be displayed in femtoseconds.
  • Frame interval (fs): time between displayed simulation frames in femtoseconds.


Fig. 2 Molecular Dynamics Options panel