In this assignment, I'd like you to use either the VMD/NAMD2 method or the MMTSB method to create an explicit water system, as discussed below.
- Add TIP3 water to a system that you have previously used, and run a simulation (a protein system, or a collection of at least 15 POPE/lipids). WARNING: this will take much longer than the unsolvated system. In this case, perform 5000 minimization steps and (at least) 5,000 dynamics steps. Save steps every 50; in other words, you will have a trajectory of at least 100 frames. Once again, the files you need to save to BioFS are
- The PSF file
- The PDB file
- The DCD file
- The control file (.nam if you use NAMD)
- Also, perform the same type of analysis from Assignment 5. If you performed an energy analysis, it will not really be comparable to your previous result. However, an RMSD and/or RDF will provide some important differences. Try and describe the differences and give a reasoned answer as to why the results are different. Data should include both a plot and the raw data. Your analysis should include some sort of actual analysis, in a written form. You should try and answer a question with your analysis. If you include a radial distribution function, for example, you might follow the path of a single water molecule somehow, and see how it fits in with the RDF data. You might try and tie energy and RMSD data together in some way. You might analyze how many amphiphile molecules are enough to act like a micelle. Your simulation data should suggest some questions for you to answer.
All necessary structure files (PSF, PDB, DCD; NAMD control file) for each stage: 20 points
Files consistent and functional: 20 points
Analysis: Plot presented clearly. data present: 10 points per analysis up to two: 20 points
Analysis: written description or analysis (2 double-spaced pages maximum): 20 points