Molecular Modeling

This page is managed by Dr. Joe Golab, and Dr. Edward Maginn (University of Notre Dame).

Syllabi, Schedules, Course Notes


textbook1 textbook2 textbook3
(contains links to exercises (contains example codes in
and case studies) Fortran90 and Python)

Open-Source Software Tools and Modeling Packages

  • Ab initio quantum software
    • GAMESS: the General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package
    • PSI4: an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties
    • NWChem: aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters
  • Molecular dynamics software
    • LAMMPS: a molecular dynamics package especially designed for materials simulations (Sandia National Laboratories)
    • GROMACS: a highly parallelized and fast molecular dynamics package with a number of analysis tools included
    • OpenMD: an open-source molecular dynamics engine that is capable of efficiently simulating liquids, proteins,
      nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. “sticky” atoms, point dipoles,
      and other coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI) and comes with a number of analysis and utility programs
    • NAMD: a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
    • HOOMD-blue: a general purpose simulation package optimized for GPUs
  • Monte Carlo software
    • Cassandra: an open-source atomistic Monte Carlo package capable of simulating any number of molecules composed of rings, chains, or both. It can be used to simulate small organic molecules, oligomers, and ionic liquids. Cassandra uses OpenMP parallelization
    • MCCCS Towhee: a Monte Carlo package that uses configurational bias and other advanced Monte Carlo moves to simulate phase equilibria and other equilibrium properties
  • Other software packages
    • Etomica: a Java API and development environment for construction and implementation of molecular simulations
    • OCTA: an integrated simulation system for soft materials
    • Avogadro: an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high-quality rendering and a powerful plug-in architecture
    • Linux4Chemistry: a list of molecular modeling tools and software packages
    • OpenMM: a high-performance toolkit for molecular simulation
    • OpenBabel: an open-source toolbox to help convert, analyze, and store data from molecular modeling packages

Databases and Resources

Useful Link

  • Computational Molecular Science and Engineering Forum (AIChE): CoMSEF is a forum for engineers and scientists who are developing and applying molecularly based theories, modeling, and simulation. This page contains links on modeling and simulation, jobs, and academic groups carrying out simulations