The Basics of Interactive Simulations: simple peptide in water

We will use UnityMol and Gromacs for this tutorial.

Start up the DECAALA-IMD-v1 exercise using the graphical interface. UnityMol will open, Gromacs will start up in the background, and the visualization will connect to the running simulation. More instructions are provided in the video walkthrough.

The peptide is shown as multi-colored hyperballs, superposed with the cartoon representation, while the water molecules are shown as white-red-white colored triangle segments.

After an initial visual exploration, you may want to get rid of the water molecules, to simplify the manipulation of the trajectory. You can achieve this from the menu, by clicking on the eye icon next to the Line title line in the model_water submenu.

When you manipulate the simulation, be gentle, otherwise the simulation will crash and you need to start over. Common tasks may be:

• try to manipulate different parts of the peptide: it’s two extremities, or a part in the middle
• observe how applied forces propagate in this system
• pull in different directions and observe the response
• try to make a knot with the peptide chain

• on the right hand side you have a python console. You can quit each tutorial by typing q() plus enter.
• you can modulate the applied force with the f(value) shortcut, where value is something in the range from roughly 0.1 to 6.0. You can check for the current value with fp().
• if you want to save the coordinates of the current scene, use s(), which writes snap.pdb in the current directory (it is indicated in the console upon saving)
• if you do not need the console, you can hide it with the arrow in a blue circle
• on the left hand side you have the main graphical menu. you can control the visualization, trajectory player speed and a few other settings, such as visual effects
• the menu can also be hidden with it’s attached arrow in a blue circle, when you don’t need it

You’ll learn:

• Hide water representations
• Adjusting pulling force
• Switch between UnityMol and Gromacs windows
• writing a snapshot to a pdb file

Click like 👍 on the video if you’re excited to get started!