Syllabus:
Molecular Dynamics
Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems
Interatomic Potentials
Energy Minimization and Related Methods for Exploring Energy Surfaces
Computer Simulation Methods
Molecular Dynamics Simulations Methods
Introduction to Coarse Graining Methods
Monte Carlo
Finite Difference Applications for PDEs
References:
- A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.
- J. M. Haile, Molecular Dynamics Simulation: Elementary Methods, Wiley-Interscience
- D. C. Rapaport , “The Art of Molecular Dynamics Simulation”, Cambridge University Press, 2004.
- W. Humphrey, A. Dalke, and K. Schulten, “VMD – Visual Molecular Dynamics”, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.
- J. C. Phillips et al., “Scalable molecular dynamics with NAMD,” Journal of computational chemistry, vol. 26, no. 16, p. 1781, 2005. “NAMD A Parallel Object-Oriented Molecular Dynamics Program”
- “LAMMPS Molecular Dynamics Simulator”. Sandia National Laboratories. Retrieved 2010-10-03.
introductory-finite-difference-methods-for-pdes
Codes
Slides:
HW:
HW4: VMD_HM
HW 5: HW5_N
HW 6: HW6N_MD
HW7: HW7_NAMD
HW8: LAMMPS