Assignment IV

Otucomes:

Develop an introductory understanding of the MD simulation procedure in Xplor-NIH

Objectives:

Perform a MD simulation of your Helix and B-sheet from assignment 2. 

Details:

  1. Minimize your structures from assignment 2
  2. Perform two MD simulation for each of your minimized structures. The first should be have initial velocities assigned base on B-M distribution at 300 K. The second should be with no initial velocities assigned.
  3. Your MD simulation must be at least 10 psec long
  4. Your trajectory must contain at least 50 frames
  5. All empirical forces must be on at the end of your MDS

Submit:

Submit four gif,mpg movies of your MD simulations.