Molecular dynamics simulations aim to describe the molecular structure, not as a rigid but rather a dynamically changing entity. The structure of flexible molecules can be described much more accurately via trajectories from molecular dynamics simulations than via conformers.
The Molecular Dynamics Plugin propagates the positions of the atomic nuclei through a molecular mechanics force-field. The resulting trajectory can be reviewed as a molecule array or animation.
- Display: display mode
- Frames: trajectory frames are displayed individually.
- Animation: trajectory is displayed as an animation.
- Forcefield: forcefield used for calculation
- Integrator: integrator type used for solving Newton's laws of motion.
- Simulation steps: number of simulation steps.
- Step time: time between simulation steps (fs).
- Initial temperature: initial temperature of the system (K).
- Start time of display: the time of the first simulation frame to be displayed (fs).
- Frame interval: time between displayed simulation frames (fs).