Syllabus:
- 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 Method
- Statistical Mechanics
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.
Slides:
Chapter 1:
Chapter 2:
Hws:
Teaching Assistant: Masoud Yousefi (masoud.yousefi71@gmail.com)
نکات مهم در ارسال تمارین:
احتراما تقاضا می شود که دانشجویان محترم درس دینامیک مولکولی جهت ایمیل تکالیف خود در قسمت عنوان ایمیل به ترتیب موارد زیر را درج فرمایند:
MD_HW?_StudentName
با تشکر
یوسفی
ایمیل:masoud.yousefi71@gmail.com
| HW (100) | Mid (120) | Final(160) | Total (20) | |
| 94107894 | 84.0 | 89 | 123 | 17.4 |
| 95201111 | 94.0 | 96 | 138 | 19.7 |
| 95207471 | 87.1 | 77 | 98 | 16.6 |
| 95209512 | 20.5 | 73 | 96 | 12 |
| 96200485 | 88.4 | 79 | 118 | 17.2 |
| 96207021 | 83.3 | 68 | 100 | 15.2 |
| 96207098 | 85.7 | 102 | 126 | 18.7 |
| 96208507 | 86.0 | 64 | 108 | 15.8 |
| 96300274 | 89.1 | 75 | 101 | 16.8 |
| 96302123 | 96.0 | 97 | 142 | 20 |