CHE 596-602 Introduction to Molecular Simulation

This course will cover the concepts behind molecular simulation methods at the quantum, atomistic, and mesoscale levels, and the practical issues that arise when using them. We will also cover the basics of running simulations in Unix/Linux-based environments, and some of the modern chemoinformatics methods that combine simulation tools with Machine Learning and Metaheuristics methods. The course will contain two tracks: a basic track for people unfamiliar with molecular simulation, and an advanced for people who already work with or do research in molecular modeling. The assignments will be different for both tracks. 3 credit hours.


• Prerequisite

For the basic track there are no formal requirements. Basic familiarity with concepts of probability and statistics, as well as basic programming, would be desirable.

For the advanced track, a graduate thermodynamics/statistical mechanics course such as CHE 713 or equivalent. Basic knowledge of quantum mechanics is desirable but not required.

• Course Objectives
  • Acquiring basic proficiency in running simulations with molecular modeling software such as Gaussian, LAMMPS, and VMD, as well as using scripts to analyze and post-process their output.
  • Being able to estimate thermodynamic and transport properties using molecular simulation software.
  • Understanding the assumptions and approximations made in modeling systems using ab initio methods, atomistic methods, and mesoscale methods, and the advantages and limitations of each.
  • Understanding the basics of modern chemoinformatics methods.

• Course Requirements

The course will involve homework assignments, which will be different for the basic and advanced tracks. Additionally, there will be a written term paper and in-class presentations where the students use one of the methods discussed. The topics and methods for the term project will be agreed upon between the individual students and the instructor.

• Textbook

There is no required textbook. Suggested references for further reading will be given throughout the semester.

• Computer and Internet Requirements

NCSU and Engineering Online have recommended minimum specifications for computers. For details, click here.

• Instructor

Dr Erik Emilio Santiso, Assistant Professor
Chemical and Biomolecular Engineering
Engineering Building I (EB1) 2100D
Box 7905
NCSU Campus
Raleigh, NC 27695

Fax: 919-515-3465