Materials modelling and computer simulation codes

2019-01-22T20:28:02Z

128.101.162.56:

The following is a sortable list (to change sort criteria click on the square icon next to the column title) of software for use in materials modelling, computer simulation and/or visualisation. ''The use of simulation software whose source code you have access to (for example, Open Source, or GNU General Public License) is a fundamental tenet of good practice, and is highly recommended'' <ref>[http://dx.doi.org/10.1063/1.476021 Wilfred F. van Gunsteren, and Alan E. Mark "Validation of molecular dynamics simulation", Journal of Chemical Physics '''108''' pp. 6109-6116 (1998)]</ref>.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! Computer program !! Focus !! class="unsortable" | Notes !! License
|-
|[[Abalone]]
|[[molecular dynamics]], visualisation
|biopolymers
|Free
|-
|[[ACEMD]]
|[[molecular dynamics]]
|biopolymers
|commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[Assemble!]]
|configuration preparation
|preparation of molecular dynamics simulations of polymeric systems
|[http://www.sciencedirect.com/science/journal/00104655 Computer Physics Communications] library
|-
|[[AVOGADRO]] [http://avogadro.openmolecules.net/wiki/Main_Page]
|visualisation
|molecule editor and visualizer
|free
|-
|[[BD_BOX]]
|[[Brownian dynamics]]
|scalable (CPU/GPU) Brownian dynamics package for UNIX/LINUX platforms
|GNU Public License
|-
|[[BOSS]]
|
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|-
|[[BRAHMS]]
|[[molecular dynamics]]
|'''B'''iomembrane '''R'''educed-'''A'''pproac'''H''' '''M'''olecular '''S'''imulator
|in development
|-
|[[CASTEP]]
|[[density-functional theory]]
|
|commercial (free in United Kingdom)
|-
|[[CCP5 Program Library]]
|various
|program library
|free to academics
|-
|[[CHARMM]]
|
|'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics
|commercial
|-
|[[CPMD]]
|[[ab initio molecular dynamics]]
|'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics
|free with [http://www.cpmd.org/cpmd_licence.html license]
|-
|[[Dalton]]
|
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|-
|[[Desmond]]
|[[molecular dynamics]]
|
|commercial, free for academics
|-
|[[DiMol2D]]
|[[molecular dynamics]]
|Molecular dynamics visualization
|free executable
|-
|[[DL_MESO]]
|[[dissipative particle dynamics]]
|Mesoscale simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license]
|-
|[[DL_POLY]]
|[[molecular dynamics]]
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|-
|[[DynamO]]
|[[molecular dynamics]]
|[[Event-driven molecular dynamics]]
|free source
|-
|[[EGO VIII]]
|[[molecular dynamics]]
|
|free
|-
|[[ENCAD]]
|[[molecular dynamics]]
|'''En'''ergy '''Ca'''lculation and '''D'''ynamics
|
|-
|[[ESPResSo]]
|[[molecular dynamics]]
|'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter
|free
|-
|[[Etomica]]
|
|development environment
|free
|-
|[[FOCUS]]
|molecular dynamics analysis
|
|
|-
|[[GALAMOST]]
|[[molecular dynamics]]
|GPU-Accelerated Large-Scale Molecular Simulation Toolkit
|free (GNU license)
|-
|[[Gaussian]]
|electronic structure
|Computational chemistry
|commercial
|-
|[[gdpc]]
|visualisation
|molecular dynamics visualisation
|free (GNU license)
|-
|[[GPEC]] [http://gpec.phasety.com]
|[[Binary phase diagrams]]
|'''G'''lobal '''P'''hase '''E'''quilibrium '''C'''alculations
|free
|-
|[[GPIUTMD]]
|[[molecular dynamics]]
|'''G'''raphical '''P'''rocessors at '''I'''sfahan '''U'''niversity of '''T'''echnology for '''M'''any-particle '''D'''ynamics
|not free, commercial
|-
|[[GROMACS]]
|[[molecular dynamics]]
|
|free source
|-
|[[GROMOS]]
|[[molecular dynamics]]
|biomolecular systems
|free for academics, fee otherwise
|-
|[[GULP]]
|[[lattice dynamics]]
|'''G'''eneral '''U'''tility '''L'''attice '''P'''rogram
|free for academics, fee otherwise
|-
|[[HOOMD]]
|[[molecular dynamics]]
|'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics.
|free, Open Source
|-
|[[IMD]]
|[[molecular dynamics]]
|
|
|-
|[[iRASPA]]
|visualisation
|
|free (Mac App Store)
|-
|[[Jmol]]
|visualisation
|
|free
|-
|[[LAMMPS]]
|[[molecular dynamics]]
|
|free source (GNU license)
|-
|[[MACSIMUS]]
|[[molecular dynamics]]
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|-
|[[MAPS]]
|simulation front-end, various
|'''Ma'''terials '''P'''rocesses and '''S'''imulations
|commercial
|-
|[[Materials Studio]]
|various
|
|commercial
|-
|[[MCCCS Towhee]]
|[[Monte Carlo]]
|
|free source
|-
|[[MCPRO]]
|[[Monte Carlo]]
|peptides, proteins, and nucleic acids in solution
|commercial
|-
|[[MDynaMix]]
|[[molecular dynamics]]
|molecular dynamics of mixtures
|free (GNU license)
|-
|[[MOIL]]
|[[molecular dynamics]]
|
|Open Source
|-
|[[Moldy]]
|[[molecular dynamics]]
|
|free
|-
|[[Molecular Workbench]]
|
|Interactive simulations
|free, Open Source
|-
|[http://dx.doi.org/10.1016/j.cpc.2016.02.025 MoRiBS-PIMC]
|[[Path integral formulation | path-integral Monte Carlo ]]
|molecular rotors in bosonic solvents
|CPC Program Library
|-
|[[Moscito]]
|[[molecular dynamics]]
|
|free (General Public License)
|-
|[[ms2]]
|[[Molecular dynamics]], [[Monte Carlo]], [[Green-Kubo relations | Green-Kubo]] formalism
|various classical ensembles
|CPC Program Library
|-
|[[Music]]
|
|'''Mu'''ltipurpose '''Si'''mulation '''C'''ode
|free (General Public License)
|-
|[[NAMD]]
|[[molecular dynamics]]
|
|free
|-
|[[NWChem]]
|
|Computational chemistry
|free
|-
|[[OCCAM]]
|[[molecular dynamics]]
|
|free
|-
|[[OpenMD]]
|[[molecular dynamics]]
|
|free - Open Source
|-
|[[ORAC]]
|[[molecular dynamics]]
|
|free
|-
|[https://dna.physics.ox.ac.uk/index.php/Main_Page oxDNA]
|[[Monte Carlo]] and [[brownian dynamics]]
|simulation code that implements coarse-grained models for DNA and RNA [http://dx.doi.org/10.1063/1.3552946]
|free (GNU General Public License)
|-
|[[Packmol]]
|[[molecular dynamics]]
|creates an initial configuration for use in simulations
|free (GNU license)
|-
|[[Peacemaker]]
|statistical thermodynamics
|Quantum cluster equilibrium calculations.
|free (GNU GPL v3)
|-
|[[PINY_MD]]
|[[molecular dynamics]]
|
|free
|-
|[[Protein Explorer]]
|visualisation
|molecular graphics
|free
|-
|[[PyMol]] [http://www.pymol.org/]
|visualisation
|molecular graphics
|commercial (academic: free)
|-
|[[Q]] [http://xray.bmc.uu.se/~aqwww/q/]
|[[molecular dynamics]]
|[[Helmholtz energy function |free energy]] calculations in [[Biological systems | biomolecular systems]]
|free with [http://xray.bmc.uu.se/~aqwww/q/q_license.pdf licence]
|-
|[[QMGA]]
|visualisation
|molecular graphics
|free source
|-
|[[RasMol]]
|visualisation
|molecular graphics
|free source
|-
|[[RedMD]]
|[[molecular dynamics]]
|'''Red'''uced '''M'''olecular '''D'''ynamics
|free, Open source
|-
|[[SageMD]]
|simulation front and back end
|
|
|-
|[[SIESTA]]
|[[ab initio molecular dynamics]]
|'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms
|free for academics, fee otherwise
|-
|[[SMMP]]
|[[Monte Carlo]]
|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins
|free (General Public License) with restrictions
|-
|[[SSAGES]]
|[[Ensembles in thermostatistics | Ensemble]] simulations
|'''S'''oftware '''S'''uite for '''A'''dvanced '''G'''eneralized '''E'''nsemble '''S'''imulations
||free (GNU / GitHub)
|-
|[[SYBYL]]
|various
|
|commercial
|-
|[[Tesla Bio Workbench]]
|
|GPU computing
|
|-
|[[TINKER]]
|
|Software tools for molecular design
|free source
|-
|[[toyMD]]
|[[molecular dynamics]]
|
|free (non-commercial)
|-
|[[UHBD]]
|[[brownian dynamics]]
|'''U'''niversity of '''H'''ouston '''B'''rownian '''D'''ynamics
|license required
|-
|[[VASP]]
|[[ab initio molecular dynamics]]
|
|
|-
|[[VMD]]
|visualisation
|Molecular dynamics visualisation in 3-dimensions
|free
|-
|[[WIEN2K]]
|
|Electronic structure calculation in solids
|commercial
|-
|[[XCrysDen]]
|visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|-
|[[XMakemol]] [http://www.nongnu.org/xmakemol/]
|visualisation
|
|free
|-
|[[X-PLOR]]
|
|Computational structural biology
|
|-
|[[YASARA]]
|
|
|free & commercial
|-
|[[YASP]] [http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html]
|[[molecular dynamics]]
|
|
|}

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[[category: Materials modelling and computer simulation codes]]

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Materials modelling and computer simulation codes