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<blockquote>
<h3> Molecular Dynamics Simulation </h3>
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 <br>
<b>"Molecular Mechanics -> Molecular Dynamics"</b><br>
(The menu entry is only enabled if a System is highlighted.)<br>
<br>
Now we have to perform some settings:<br>
Set the number of iterations to 100.<br>
To accelerate the MDS, set the timestep to 0.001. <br>
Set the temperature to 400 K.<br>
Select the force field "<b>AMBER</b>".<br>
<br>
Also, we want to be able to visualise the resulting trajectories.
To do so, click the checkbox <b>save to</b>.
Then click <b>"Simulate"</b>.
<br>
The next step becomes available, when the simulation has finished
and a trajectory file was created.
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Press Next to continue.
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