Molecular Modeling

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

Syllabi, Schedules, Course Notes

Molecular Simulation: syllabus, class notes, simulations (University of Buffalo)
A Self-Guided Introduction on Theoretical Chemistry (University of Utah)

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

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

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

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

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

ExPASy: a bioinformatics portal
Worldwide Protein Databank: a collection of protein structures
Knowledgebase of Interatomic Models: collects and validates potentials, mainly for the solids modeling community
NNIN/C Pseudopotential Virtual Vault:: a database of over 1100 pseudopotential or PAW files. Pseudopotentials are available for Abinit, Quantum Espresso, Qbox, and Siesta
National Institute of Standards and Technology (NIST)

NIST Interatomic Potentials Repository Project: a collection of interatomic potentials
NIST Standard Reference Simulation Website: aims to provide well-documented simulation results for a variety of systems from various simulation techniques
NIST Chemical Informatics Research Group: useful links for chemical informatics research
Computational Chemistry Comparison and Benchmark Database (CCCBD): experimental and computational thermochemical data for a large number of gas-phase atoms and molecules. Tools for comparing experimental and computational ideal-gas thermochemical properties

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