The Basics of Interactive Simulations: coarse-grained membrane patch

We will use UnityMol and Gromacs for this tutorial.

Start up the vamp-cg-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 will be provided live during the session.

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 Point title line in the model_water submenu.

The peptide is multi-colored, one lipid molecule is colored in green, one ion is colored in yellow. All other molecular species, in particular the lipid bilayer, are in white.

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

• try to extract the peptide out of the bilayer. Is it doable?
• try to pull out the lipid a little, see how easily it slips back in, then pull it out completely
• how do the lipid and peptide membrane anchoring compare?
• try to pull the ion through the bilayer

• on the right hand side you have a python console. You can quit each tutorial by typing q() plus enter.
• other than for quitting or starting up (usually with the go() command, you will not really 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:

• Manipulating the view
• Changing representations, hiding, deleting and creating them
• Pulling on atoms and tuning your applied force

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