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Molecular Modeling

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Syllabi, Schedules, Course Notes

Textbooks

textbook1 textbook2 textbook3 

Additional textbooks

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
  • RASPA2 Classical molecular simulation code

Other software packages and utilities

  • 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
  • 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
  • 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

Other resources

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

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