Introduction

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

Options

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