Molecular Modeling

General Information

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

Open Source Software Tools and Modeling Packages

 

  • Etomica – Etomica is a Java API and development environment for construction and implementation of molecular simulations.
    http://www.etomica.org/

  • OCTA – OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry (METI), Japan.
    http://octa.jp/

  • GAMESS – The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
    http://www.msg.ameslab.gov/GAMESS/GAMESS.html

  • LAMMPS – a molecular dynamics package developed at Sandia National Laboratories especially designed for materials simulations.
    http://lammps.sandia.gov/

  • NWChem – 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. http://www.nwchem-sw.org/index.php/Main_Page

  • PSI4 – PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. http://www.psicode.org/index.php

  • Cassandra – Cassandra is an open source atomistic Monte Carlo package capable of simulating any number of molecules composed of rings, chains, or both. It can be used it to simulate small organic molecules, oligomers, and ionic liquids. Cassandra uses OpenMP parallelization and comes with a number of scripts, utilities and examples to help with simulation setup. http://cassandra.nd.edu/

  • MCCCS Towhee – a Monte Carlo package that utilizes configurational-bias and other advanced Monte Carlo moves to simulate phase equilibria and other equilibrium properties.
    http://towhee.sourceforge.net/

  • GROMACS – a highly parallelized and fast molecular dynamics package with a number of analysis tools included.
    http://www.gromacs.org/

  • OpenMD – OpenMD is an open source molecular dynamics engine which 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 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 that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.
    http://openmd.org/

  • NAMD – NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
    http://www.ks.uiuc.edu/Research/namd/

  • Avogadro – Avogadro is 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 plugin architecture.
    http://avogadro.cc/wiki/Main_Page

  • PyMol – A molecular visualization system on an open source foundation, maintained
    and distributed by Schrödinger
    http://www.pymol.org/

  • Linux4chemistry – huge list of molecular modeling tools and software packages
    http://www.linux4chemistry.info/

Databases and Resources

 

  • ExPASy – A bioinformatics portal

http://www.expasy.org/

  • Computational Chemistry Comparison and Benchmark Database (CCCBD)
    Experimental and computational thermochemical data for a selected set of 1591 gas-phase atoms and molecules. Tools for comparing experimental and computational ideal-gas thermochemical properties.
    http://cccbdb.nist.gov/

  • Worldwide Protein Databank – A collection of protein structures.
    http://www.wwpdb.org/

  • NIST Interatomic Potentials Repository Project – A collection of interatomic potentials.
    http://www.ctcms.nist.gov/potentials/

  • Knowledgebase of Interatomic Models – An NSF-sponsored project that collects and validates potentials, mainly for the solids modeling community
    https://openkim.org/

  • NIST Virtual Vault for Pseudopotentials and PAW Datasets – A resource to provide information on pseudopotentials relevant for electronic structure calculations of molecules, materials, and nanostructures.
    http://www.nnin.org/research-support/computation/nnin-computation-nanotechnology-resources/virtual-vaults

  • NIST Standard Reference Simulation Website – The Standard Reference Simulation Website is an ongoing project whose aim is to provide well-documented simulation results for a variety of systems and from various simulation techniques. The results contained here are usually generated in-house at NIST but, when certain criteria are satisfied, may also include results from provided from outside collaborators.
    http://www.nist.gov/mml/csd/informatics_research/srsw.cfm

  • NIST Chemical Informatics Research Group – Many useful links for chemical informatics research
    http://www.nist.gov/mml/csd/informatics_research/

Educational Resources