| 1. Please load the Martini coarse-grained simulation file from "ras-raf-membrane/data/ras-raf-membrane.gro" into VMD. The simulations has a membrane and a RAS-RAF protein complex. | |
| 2. Use VMD to show a zoomed in side view of the membrane and center on the protein with the protein below the membrane. | |
| For the bilayer only show the PO4 lipids beads and ROH cholesterol bead and color them gray. | |
| Also show the protein back bone beads coloring RAS (resid 2 to 187) red and RAF (resid 188 to 329) blue. | |
| Take a screenshot of the visualization. | |
| 3. Analyze the visualization and answer the following questions: | |
| Q1: Are there any cholesterol head groups in the bilayer center? (yes/no) | |
| Q2: How many lipids are there within 1.5 nm of the RAF protein? | |
| A. 0 | |
| B. 0-3 | |
| C. 3-5 | |
| D. >5 | |
| 4. Save your work: | |
| Save the VMD state as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.vmd". | |
| Save the screenshot of the visualization as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.png". | |
| Save the answers to the analysis questions in plain text as "ras-raf-membrane/results/{agent_mode}/answers.txt". |