Molecular Dynamics Plugin

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.

images/download/attachments/1806658/md.png

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.

images/download/attachments/1806658/mddialog.png

Fig. 2 Molecular Dynamics Options panel