Due Thursday, Aug. 18, (Wednesday at midnight)
Updated July 14, 2022.
Use NAMD GUI to generate a solvated simulation of a small (< 5000 Da) protein from the protein data bank (It is OK to re-use an example you have already worked on!). Once you have successfully performed the simulation with NAMD GUI, perform the following analysis using VMD:
- Plot the total energy of the system to make sure it is equilibrated. How can you tell if it has reached equilibrium?
- Plot the RMSD of the protein compared to the RCSB starting structure. How does it compare? Is the protein relatively static in its structure, or does it fluctuate between some different conformations?
- Describe the strengths and weaknesses of the NAMD GUI system. How is it better or worse than running NAMD and preparing files with VMD?