Molecular Dynamics Plugin

    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