Molecular Dynamics

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:

  1. A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.
  1. J. M. Haile, Molecular Dynamics Simulation: Elementary Methods,  Wiley-Interscience
  1. D. C. Rapaport , “The Art of Molecular Dynamics Simulation”, Cambridge University Press, 2004.
  1. W. Humphrey, A. Dalke, and K. Schulten, “VMD – Visual Molecular Dynamics”, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.
  1. 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”
  1. “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

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