Introduction to MD simulations

Introduction to MD simulations

Introduction to MD simulations



  • Mathematical background
  • Physical background
  • Statistical analysis

Learning Objectives:

  • Build the necessary background to understand the theory behind MD simulations.

Learning Outcomes:

  • Understand why we need MD simulations.
  • Understand the mathematical concepts of coordinate systems, series expansion, vectors, matrix notations, and complex numbers.
  • Understand the meaning of potential energy and potential energy surface.
  • Understand the difference between statistical average and true average
  • Understand the basic statistical analysis to analyze MD trajectories.
Language:  English

Trainer: Prof. Dr. Khaled Barakat, Faculty of Pharmacy, University of Alberta, Edmonton, Canada

Dr. Barakat received his PhD in biophysics from the University of Alberta in 2012 followed by a postdoctoral fellowship in the lab of the Nobel Laureate, Professor Michael Houghton, for two years.  Dr. Barakat’s research stands at the multidisciplinary interface of physics, biology and computer science. His research is focused on understanding the structure-function-relationship of cardiac ion channels in health and disease and on developing and applying state-of-the-art computational drug discovery tools to discover new antiviral and immunotherapeutic small molecule drugs. During his career, Dr. Barakat received numerous awards including the CIHR and AIHS postdoctoral fellowships, the prestigious UofA dissertation award, the ACRI Studentship and many distinction awards throughout his undergraduate and graduate studies. Dr. Barakat is also the editor of a number of journals. Throughout his research career, Dr. Barakat’s lab has been supported by different funding agencies including the Alberta Cancer Foundation, Li Ka Shing Applied Virology Institute, Natural Sciences and Engineering Research Council (NSERC), Li Ka Shing Institute of Virology and IC-IMPACTS Centers of Excellence. Dr. Barakat is also the CEO & co-founder of HEKA Therapeutics Inc. and co-founder of ACHLYS; two spinoff companies devoted to drug discovery of immune checkpoints small molecule inhibitors and predicting off-target toxicity of new compounds in drug discovery.