Molecular Modeling

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Syllabi, Schedules, Course Notes

• Molecular Simulation (University of Buffalo): syllabus, class notes
• Elementary Quantum Chemistry and Machine Learning (University of Buffalo)
• A Self-Guided Introduction on Theoretical Chemistry (University of Utah)
• Modern Molecular Simulation Methods (University of California Santa Barbara)
• Computational Chemistry (University of Notre Dame)
• Applications of DFT (Clemson University)
• Computational Chemistry (University of Minnesota): 49 videos

Textbooks

Additional textbooks

• Molecular Modeling and Simulation: An Interdisciplinary Guide by Tamar Schlick
• Molecular Modelling: Principles and Applications by Andrew Leach 
• The Art of Molecular Dynamics Simulation by D.C. Rapaport

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 (GitHub files): 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 (GitHub files): 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
• RASPA2 Classical molecular simulation code
• GOMC (GitHub files): an open-source software for simulating molecular systems using the Metropolis Monte Carlo algorithm. The software has been written in object oriented C++, and uses OpenMP and NVIDIA CUDA to allow for execution on multi-core CPU and GPU architectures. GOMC employs widely-used simulation file types (PDB, PSF, CHARMM-style parameter files) . GOMC can be used to study vapor–liquid equilibria, adsorption in porous materials, surfactant self-assembly, and condensed phase structure for complex molecules. 

Other software packages and utilities

• Etomica: a Java API and development environment for construction and implementation of molecular simulations
• Etomica Modules: instructional modules based in molecular simulations
• OCTA: an integrated simulation system for soft materials
• ABINIT: density function theory for material science
• 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
• CP2K: quantum chemistry and solid state physics program package
• OpenMM: a high-performance toolkit for molecular simulation
• OpenBabel: an open-source toolbox to help convert, analyze, and store data from molecular modeling packages
• Free energy methods (Alchemistry.org) employs unphysical ("alchemical") intermediates to estimate the free energies of various physical processes
• Force fields (openforcefield.org) An open source, open science, and open data approach to better force fields
• QBox: atomic-scale simulations of molecules, liquids, and solids
• Quantum EXPRESSO: first-principles electronic-structure calculations and materials modeling
• SIESTA: electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
• Simulation setup, automated force field generation and job management (mosdef.org) a set of Python tools designed to facilitate the initialization, atom-typing, and screening of soft matter systems using molecular dynamics simulations. 
• Simulated Environment for Atomistic and Molecular Modeling (SEAMM) composed of plug-ins for other software packages so users can create simulation scripts that combine those programs
• MDAnalysis (GitHub files): an object-oriented Python library to analyze molecular dynamics trajectories

Other resources

• LiveComms living journal 
• Molecular Simulation Sciences Software Institute (MolSSI)

Databases and Resources

• 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
• PNNL Basis set exchange:
• 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
  • NIST WebBook: data compiled by NIST

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