• ComputationalChemistryActivity
• GradSchoolCourse

ComputationalChemistryActivity

GradSchoolCourse

Syllabus | Structure | Lectures | Coursework

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. Course to be run over the Access Grid using speakers from both Edinburgh and St. Andrews Universities.

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

• Six one-hour or two-hour lectures
• Four practical assignments

Lectures

Lecture 1 - Introduction to Computational Chemistry

• Tanja van Mourik 2 hours

• Theory and methods
  • HF and SCF
  • Electron correlation - MP2, CI, CC, MCSCF
  • DFT
  • Semi-empirical
  • Classical simulation
• Pros and cons
• Cheminformatics

Lecture 2 - HPC, Linux and vi

• Andy Turner 1 hour

• 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
• Principles of HPC
  • Parallel computing
  • Batch submission
  • Grid

Lecture 3 - Molecular electronic structure codes: Gaussian 03, MOLPRO, GAMESS-UK

• Herbert Fruchtl 2 hours?

• Specifying the geometry
  • Molecule builders
  • z-matrices
  • Adding constraints
• Specifying the method and basis
• Calculation types
  • Geometry Optimization
  • TS Optimization
  • Conformational analysis
  • Frequencies
  • Properties and MOs
  • Reaction Pathways
  • Solvation methods - implicit and explicit solvation
• Restarting calculations

Lecture 4 - Periodic electronic structure codes: CASTEP, CPMD

• Carole Morrison 1 hour

• Generating input
  • Specifying the structure
  • Specifying the pseudopotential
• Running calculations
  • Single point energy
  • Structure optimization
  • Molecular dynamics
• Restarting claculations
• Analyzing the results

Lecture 5 - Classical simulation codes - Amber, DL_POLY

• Andy Turner 2 hours?

• Generating input
  • Specifying the force field
  • Generating the starting coordinates
• Equilibrating/optimizing the system
• Conformational analysis
• Docking
• Biological systems
• Generating results
• Analyzing the results

Lecture 6 - Visualization

• Herbert Fruchtl 1 hour

• Programs available
• Visualizing electronic structure results
  • Geometries
  • Surfaces - MOs, electrostatic potentials, spin density
  • Vibrational frequencies
• Visualizing periodic electronic structure results
• Visualizing classical simulation results
  • Trajectories
  • Using visualization as an analysis tool
  • RMSD

Coursework

Assignment 1 - Linux and vi

Have a go at linux command line and vi editor

Assignment 2 - Molecular electronic structure

Build molecules for input into electronic structure code. Run job. Check output

Assignment 3 - Periodic electronic structure

Create input for program of your choice. Submit job. Check output

Assignment 4 - Classical simulation

Do a molecular simulation of some sort and view the trajectory

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