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

# 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