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