Reference no: EM1376943
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.
|
Prepare journal entries to record liquidation transactions
: Prepare journal entries to record these liquidation transactions - When the liquidation commenced, expenses of $20,000 were anticipated as being necessary to dispose of all property. Prepare a predistribution plan for the partnership.
|
|
Explanation of sexual harassment
: Provide your opinion on this case of sexual harassment where a managing director of defendant had hanging in his office a poster of 50 or so women on motorcycles naked;
|
|
Pitfalls of job evaluation methods
: Explain a condition in which it would not be effective for the business. For example, when would ranking be either impractical or unjust?
|
|
Perspective of appraisals
: Describe your experience with performance appraisals and overall, have you discovered them motivating, de-motivating, a waste of time, or invaluable?
|
|
Computational biophysics and nanoscale simulations
: Write the formula of the root-mean-square deviation (RMSD) between two molecular structures - Computational Biophysics and Nanoscale Simulations
|
|
Determine the potential penalties
: Can you give me your opinion on this, The CFO comes up to you one night and asks you to go out for a drink with her.
|
|
Policy change memo
: Make a memo to an appropriate policy decision creator requesting a change in Single Payer Healthcare organization. The memo should identify shareholders
|
|
Executive compensation in a nonprofit organization
: Suppose you are a part of the Board of Directors for a non-profit organization. A new executive director has just been employed. The previous executive director received a payment and no variable pay.
|
|
Possible violations against blacks
: It is found that, at a health club, owner has been putting a notation on application of black membership applicants that reads DNWAM, which means do not wish as member.
|