> ### Molecular Dynamics Simulation

> Now we will simulate the peptides natural movements by performing a molecular dynamics simulation (MDS). To do so, open the according dialog by using the menu entry
> "Molecular Mechanics -> Molecular Dynamics"
> (The menu entry is only enabled if a System is highlighted.)
> Now we have to perform some settings:
> Set the number of iterations to 100.
> To accelerate the MDS, set the timestep to 0.001.
> Set the temperature to 400 K.
> Select the force field "AMBER".
> Also, we want to be able to visualise the resulting trajectories. To do so, click the checkbox save to. Then click "Simulate".
> The next step becomes available, when the simulation has finished and a trajectory file was created.
> Press Next to continue.