Project instructions

Requirements:

• Project must use an advanced MD method
• Apply an advanced sampling technique

• Do a free-energy calculation
• Derive/improve force-field parameters
• ...
• Ideally should be applied to a system you are already working on
• You can use any MD code you want

 Project report:
• Short description of the system
• What do you expect to get out of the application of the advanced method
• Description of the base MD setup: force field, cut-off, electrostatics, unit cell, thermo/barostat params, etc
• Analysis of the method, including error estimates (simple way: apply the method multiple times with different initial cond.)
• Did the method help for your system?
Thursday 15 May 14
 
Examples
• Replica exchange
• Umbrella sampling
• Metadynamics
• Solvation/binding free-energy
• Coarse graining (part of) a system
• Non-equilibrium dynamics (not in lectures) • Improve partial charges and/or LJ params.