Tutorial dialog

# 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.