Computational Biophysics and Nanoscale Simulations
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
1. (i) Write the formula of the root-mean-square deviation (RMSD) between two molecular structures.
(ii) Define the Euler angles, and explain briefly why are they relevant in comparing two protein conformations. Please use no more than one hundred words!
2. Using NAMD and the configuration files for the simple simulation of the decaalanine molecule Ala10, run a short simulation for N=520,000 steps, using a time step of 2 fs and write the data in a DCD trajectory file every 2,000 steps. As we did in the class, you can control the "temperature" of your system in order to induce the unfolding of deca-alanine. One way to do this is by adding two more lines at the end of your alanin.namd script, for example:
langevin on
langevinTemp 310.0
Run three simulations corresponding to "temperature" values of 310K, 510K and 710K. As before, each run should only take about 5 or 6 minutes on a regular PC. You can use the files provided online in Ala10_hw2.zip as examples on how to setup and run your small simulations. If you are using NAMD on a PC under Windows, you can run the simple script file named "namdrun.bat" (after changing it accordingly).
Using the VMD program, load and visualize each of the three trajectories, for each of the three temperatures. Extract and plot the end-to-end distance dE-E (defined as the distance between the first and the last Cα atoms) versus time. Please remember to label the axes correctly.
3. Using the VMD program and its RMSD Trajectory Tool, calculate and save the data for the Cα-RMSD values along the deca-alanine trajectory, calculated using as reference the first, starting frame. Please remember to align each trajectory to the first frame before calculating the Cα-RMSD values. Plot the Cα-RMSD values for all three aligned trajectories corresponding to the three different temperatures on the same graph.
4. Compare the two graphs (i.e., for dE-E and Cα-RMSD, each of them showing three curves corresponding to T= 310K, 510K and 710K), and state which of these three measures (d or C ) captures better the "unfolding" process of Ala10.