Due Monday, August 22, 12:00 AM (Sunday at midnight)
Updated July 14, 2022
Perform an SMD simulation and collect data. Using one of the molecules in the SMD Lab, implement the following:
- Generate a matched PSF/PDB pair for the simulation, molecule only, no water or other solvent.
- Generate 5 different PDB files from an equilibration simulation
- For one of these PDB files, specify the fixed and pulled atoms, and put this information into the smd.tcl file
- Properly prepare the xxx_SMD.conf file — the NAMD configuration file for your molecule
- Successfully run a simulation which pulls your molecule.
The files you need to provide are:
- The PSF and PDB for the equilibration simulation, and the corresponding NAMD configuration file (3 files)
- The single PDB file from the equilibration simulation
- The smd.tcl and xxx_SMD.conf files which properly run the pulling simulation (with the atomic coordinate information properly specified)
- The xxx_smd_tcl.out file which shows the force data.
- (Do not submit the DCD files, as they will be quite large, and the force data is the main goal here.)
The method of grading will be to run the above steps in sequence and successfully produce the force data.
(This assignment could serve as a starting point for the final project, due at the end of Week 5. Success in this assignment will ensure the final project goes smoothly.)