Master course in molecular simulations (MSI)

Synopsis

The focus of this course is to provide the tools, knowledge and practical experience to perform computational experiments on proteins and other small molecules (drugs) in-silico using molecular dynamics simulations on a high performance computing infrastructure.

  • Target students
  • Students with an interest in computing, simulation, programming, computational biophysics and biochemistry.
  • Requirements
  • Programming: Use of medium to high level Python is used in order to perform analysis on large simulation data sets.
  • Knowledge: Interdisciplinar, but chemistry, biotechnology, physics and computer science will be an advantage.
  • Practical information
  • Course length is 30 hours of classes (corresponding to 100 hours of personal work including classes) of which 4 hours are for the final project revision and defence. Room: all lectures will be in Aula 61.212
  • Evaluation
  • 50% of final evaluation is based on small projects during the course
  • 50% of final evaluation is based on a a final project carried out in group
  • Useful books
  • Computer Simulation of Liquids, Allen and Tildesley.
  • Understanding Molecular Simulation, Second Edition: From Algorithms to Applications, Frenkel and Smit.
  • Lecturers: gianni.defabritiis-at-upf.edu
  • Resources and software
  • HTMD documentation: https://www.htmd.org
  • VMD userguide: http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html

Course material

  • Day 1: Introduction to molecular dynamics
  • Introduction to molecular dynamics
  • Force fields (bond, angle, dihedral, improper, Lennard-Jones, Coulomb)
  • Proteins and water

  • Day 2: Learning VMD
  • Check VMD installation
  • Learning the user interface
  • Manipulating molecules
  • Resources

  • Day 3: Methods in molecular dynamics
  • Introduction to methods
  • Practice on using acemd

  • Day 4: Intro to Git
  • An introduction to git
  • github.com

  • Day 5: Learning HTMD
  • Working with HTMD
  • The Molecule object, methods and attributes
  • Visualization using webgl
  • Basic operations

  • Day 6: Building Systems with HTMD
  • System building basics using HTMD tutorial
  • System building for Benzamide-Trypsin
  • System building for mu opioid GPCR

  • Day 7: System Building exercise and introduction to Ligand Binding Analysis
  • System Building for Protein-Protein Interactions (Barnase-Barstar)
  • Introduction to the Ligand Binding Analysis tutorial

  • Day 8: Markov Models Class and Ligand Binding Analysis
  • Presentation introducing the workflow of building Markov models
  • Practise with the Ligand Binding Analysis tutorial of Benzamidine-Trypsin

  • Day 9: Ligand Binding and Protein Folding Analysis
  • Protein Folding Analysis - Villin
  • Presentation of the 2nd project

  • Day 10: Conformational analysis of a protein
  • Practise with the conformational tutorial

  • Day 11: Markov state models
  • A short introduction on Markov state models

  • Day 12: Ligand parameterization
  • Tutorial on ligand parameterization using QM methods

  • Day 13: Seminar

  • Day 14: Project progress

  • Day 15: Project progress

Small projects