Syllabus | Structure | Location | Lectures
A Practical Introduction to Computational Chemistry
Aims
A practical course to introduce graduate chemistry students (and other chemistry researchers) to computational chemistry techniques. The course will particularly referenced to EaStCHEM RCF facilities but the concepts and skills gained will be generally applicable.
Syllabus
Basic theory behind ab initio, DFT, semi-empirical and classical techniques
- Introduction to HPC facilities and batch queueing systems
- Introduction to Linux and vi
- Using molecular electronic structure codes - Gaussian, GAMESS-UK and MOLPRO
- Using periodic electronic structure codes - CASTEP and CPMD
- Using classical simulation codes - Amber and DL_POLY
- Using visualization tools to analyze the results
Structure
- Seven one hour or two hour lectures
Location
The course will use the SUPA VC rooms. Their locations are:
Edinburgh - 6224 JCMB, Kings Buildings
St Andrews - 307, Physics Building
Dundee - Basement, Kelvin Building
Glasgow - 255a, Kelvin Building
Heriott-Watt - 1.27, Earl Mountbatten Building
Paisley - F.318, Henry Building
Strathclyde - 813, John Anderson Building
Lectures
Lecture 1 - Introduction to Computational Chemistry I
Tanja van Mourik (School of Chemistry, University of St. Andrews)
3-4pm Wednesday 24 October 2007, 1 hour
This lecture will give an overview of electronic structure methods and concepts. The following topics will be covered:
- Ab initio methods
- The Hartree-Fock (HF) method
- Configuration Interaction (CI)
- The multi-configurational self-consistent field (MCSCF) method
- Coupled cluster (CC) methods
- Møller-Plesset perturbation theory
- Density functional theory (DFT)
- Semi-empirical methods
- Basis sets
- Electron correlation
- Basis set superposition error (BSSE)
Lecture 2 - Introduction to Computational Chemistry II
Tanja van Mourik (School of Chemistry, University of St. Andrews)
3-4pm Wednesday 31 October 2007, 1 hour
This lecture will give an (incomplete…) overview of the broad area of cheminformatics. The following methods will be discussed:
- Force field methods
- Molecular dynamics (MD)
- Molecular docking
- QSAR
Lecture 3 - Introduction to High-Performance Computing and Linux
Andy Turner (School of Chemistry, University of Edinburgh)
3-4pm Wednesday 7 November 2007, 1 hour
This lecture will provide a brief introduction to the concepts of both high performance and grid computing. In addition it will provide a practical introduction to the Linux command line and Vi text editor; both of which are ubiquitous on these types of facilities. We will focus on the Linux and Vi commands that will be useful for running the software covered in the course.
High Performance Computing
- Parallel computing
- Batch submission
Grid Computing
- Differences from HPC
Linux
- The Linux command line
- Filesystem organization and management
- Useful commands (e.g. less, tail, grep, find)
Vi
- The two modes
- Editing
- Closing and saving
- Tips and Tricks
Remote access
- SSH and SFTP
- ASCII and binary transfer
Lecture 4 - Molecular Electronic Structure Software
Herbert Fruchtl (School of Chemistry, University of St. Andrews)
3-5pm Wednesday 14 November 2007, 2 hours
Lecture 5 - Classical Simulation Software
Andy Turner (School of Chemistry, University of Edinburgh)
3-5pm Wednesday 21 November 2007, 2 hours
This lecture will provide an introduction to the world of empirical computational chemistry. These methods are the only practical option for many systems including the amorphous condensed phase and biopolymers. The lecture will focus on the practical aspects of using the software rather than the mathematics behind it.
Introduction to empirical force-field methods
- Differences from ab initio methods
- Programs available (DL_POLY, Amber)
- Periodic boundary conditions
Building the input
- Generating the starting configuration
- Specifying the force field
Equilibrating/optimizing the system
- Removing bad contacts
- How do we know everything is OK?
Generating results and analysis
- Production runs
- Analysis techniques
Applications
- Conformational analysis
- Dynamic analysis
- Docking
- Biological systems
Lecture 6 - Periodic Electronic Structure Software
Carole Morrison (School of Chemistry, University of Edinburgh)
3-4pm Wednesday 28 November 2007, 1 hour
This lecture will build on the earlier material presented in the course to discuss the special challenges faced when simulating condensed phases.
- The practicalities - basis sets, levels of theory, k-point sampling.
- Geometry optimisation and molecular dynamics
- Software packages - what is available, and what they can do.
- Where to go from here
Lecture 7 - Visualization Software
Herbert Fruchtl (School of Chemistry, University of St. Andrews)
3-4pm Wednesday 5 December 2007, 1 hour