Assignment 8, the Final Project is due Friday, August 26 at 11:59 PM



If you choose to perform an SMD simulation, you will need to run (at least) five simulations of 50,000 time steps and average the results of the force calculations to submit as your final experimental measurement. The steps here are spelled out on the SMD Laboratory page. They are:


  1. Create a matched PSF/PDB pair
  2. Perform an equilibration simulation, from which you will extract the (at least) five starting structures
  3. (for each starting structure) Identifying likely anchor (fixed atom(s)) candidates and pulled atom(s)
  4. (for each starting structure) Use VMD to collect labeling information on these atoms (resname, name, index, etc)
  5. (for each starting structure) Insert the necessary lines into a NAMD control file which will identify the simulation as an SMD simulation
  6. (for each starting structure) Create a TCL file that specifies necessary parameters
  7. Create multiple copies of the simulation, and running them in sequence
  8. Processing the individual results, and combining the data into one "averaged" result
The files necessary in this submission would be:
  • The initial PSF/PDB
  • The five starting SMD PDB files
  • The five stating control files
  • The five smd.tcl files
  • The five DCD files
  • The tcl_smd.out files
  • The averaged data
  • any shell scripts used
(The easiest way to accomplish this is through an "tar" archive. See the video lecture for how to do this.)

The grading will be based upon:
  • Submission of the files: 10 points
  • Preparing and running five simulations: 5 points by hand, 10 points by using a shell script
  • Five independent (i.e. different starting points, thus different) simulations: 10 points
  • Appropriate pulling velocity for 50,000 steps: 10 points
  • Force data for each of five simulations: 10 points
  • Averaged force data plotted w/ the five individual simulations data, and analysis: 20 points

The analysis should be a description of the secondary structural features, the order they seem to be lost as the protein is pulled, and your reasoning as to why this order is followed.

If you choose to perform a solvation simulation, you need to prepare your solvated protein simulation should contain a water box large enough to provide at least 7 angstroms of water "padding" around your protein on all sides. The simulation requires at least 100,000 time steps. The rough steps needed are:


  1. Create a matched PSF/PDB pair
  2. Perform an initial minimization, and then equilibration simulation of at least 10,000 steps
  3. Create a water box around the protein (as above), and generate a new PSF/PDB
  4. Properly heat and equilibrate this larger system
  5. Perform at least 100,000 time steps of molecular dynamics
  6. Perform the following post-processing/data collection: a) RMSD of the alpha carbons (compared with the initial structure from the protein data bank or initial structure) over the 100,000 time steps. b) Determine what percent of the water molecules are within 3 A of the protein over the course of the simulation c) Perform radial distribution function calculations for c1: protein-water and c2: water-water oxygen atoms.

The files necessary in this submission would be

  • The initial PSF/PDB
  • The solvated PSF/PDB
  • The NAMD control file used to run the equilibration
  • The NAMD control file used to run the long simulation
  • The DCD file from the long simulation
  • The output/data files from the analysis
  • Discussion of the output/data files
(The easiest way to accomplish this is through an "tar" archive. See the video lecture for how to do this.)

The grading will be based upon:
  • Submission of the files: 15 points
  • Preparing and running the first equilibration simulation: 15 points
  • Preparing the solvated protein structure: 10 points
  • Running the second solvated simulation of at least 100,000 time steps: 20 points
  • Data analysis section: 20 points

The analysis should be a discussion based upon RMSD (how stable is the structure? If there is any change in the structure, does the RMSD show it?), water structure around the protein (is water more structured, or less structured than plain old bulk water?), and radial distribution function (which can help with the water structure analysis).