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| 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>. | | The following is a sortable list (click on the icon next to the column title) of software |
| {| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0" | | {| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0" |
| |- | | |- |
| ! Computer program !! Focus !! class="unsortable" | Notes !! License | | ! 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]] | | |[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]] |
| |[[molecular dynamics]] | | | |
| |Assisted Model Building with Energy Refinement | | |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]] | | |[[BOSS]] |
| | | | | |
| | '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem | | | '''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]] | | |[[CASTEP]] |
| |[[density-functional theory]] | | | [[Density-functional theory]] |
| | | |
| | | | | |
| |commercial (free in United Kingdom)
| |
| |- | | |- |
| |[[CCP5 Program Library]] | | |[[CCP5 Program Library]] |
| |various | | | |
| |program library | | | |
| |free to academics | | | |
| |- | | |- |
| |[[CHARMM]] | | |[[CHARMM]] |
| | | | | |
| |'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics | | |'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics |
| |commercial | | | |
| |- | | |- |
| |[[CPMD]] | | |[[CPMD]] |
| |[[ab initio molecular dynamics]] | | | |
| |'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics | | |'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics |
| |free with [http://www.cpmd.org/cpmd_licence.html license] | | | |
| |- | | |- |
| |[[Dalton]] | | |[[Dalton]] |
| | | | | |
| |Computational chemistry | | |Computational chemistry |
| |free with [http://www.theochem.kth.se/dalton/ license]
| |
| |-
| |
| |[[DeePMD-kit]] [http://www.deepmd.org/]
| |
| |[[molecular dynamics]]
| |
| | deep learning based modelling of interatomic potential energy and force field and to perform MD
| |
| | GNU Lesser General Public License v3.0
| |
| |-
| |
| |[[Desmond]]
| |
| |[[molecular dynamics]]
| |
| | | | | |
| |commercial, free for academics
| |
| |- | | |- |
| |[[DiMol2D]] | | |[[DiMol2D]] |
| |[[molecular dynamics]] | | | |
| |Molecular dynamics visualization | | |Molecular dynamics visualization |
| |free executable | | | |
| |- | | |- |
| |[[DL_MESO]] | | |[[DL_MESO]] |
| |[[dissipative particle dynamics]] | | | |
| |Mesoscale simulation package | | |Mesoscale simulation package |
| |free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license] | | | |
| |- | | |- |
| |[[DL_POLY]] | | |[[DL_POLY]] |
| |[[molecular dynamics]] | | |[[Molecular dynamics]] |
| |Molecular simulation package | | |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]] | | |[[ESPResSo]] |
| |[[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 | | |'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter |
| |free
| |
| |-
| |
| |[[Etomica]]
| |
| | | | | |
| |development environment
| |
| |free
| |
| |- | | |- |
| |[[FOCUS]] | | |[[Gaussian]] |
| |molecular dynamics analysis
| |
| | | | | |
| | |Computational chemistry |
| | | | | |
| |-
| |
| |[[GALAMOST]]
| |
| |[[molecular dynamics]]
| |
| |GPU-Accelerated Large-Scale Molecular Simulation Toolkit
| |
| |free (GNU license)
| |
| |-
| |
| |[[Gaussian]]
| |
| |electronic structure
| |
| |Computational chemistry
| |
| |commercial
| |
| |- | | |- |
| |[[gdpc]] | | |[[gdpc]] |
| |visualisation | | | |
| |molecular dynamics 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]] | | |[[GROMACS]] |
| |[[molecular dynamics]] | | |[[Molecular dynamics |Classical molecular dynamics]] |
| | | |
| | | | | |
| |free source
| |
| |- | | |- |
| |[[GROMOS]] | | |[[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]] | | |[[HOOMD]] |
| |[[molecular dynamics]] | | | |
| |'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics. | | |'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics. |
| |free, Open Source | | | |
| |- | | |- |
| |[[IMD]] | | |[[IMD]] |
| |[[molecular dynamics]] | | |[[Molecular dynamics |classical molecular dynamics]] |
| |
| |
| |
| |
| |-
| |
| |[[iRASPA]]
| |
| |visualisation
| |
| | | | | |
| |free (Mac App Store)
| |
| |-
| |
| |[[Jmol]]
| |
| |visualisation
| |
| | | | | |
| |free
| |
| |- | | |- |
| |[[LAMMPS]] | | |[[LAMMPS]] |
| |[[molecular dynamics]] | | |[[Molecular dynamics]] |
| | | |
| | | | | |
| |free source (GNU license)
| |
| |- | | |- |
| |[[MACSIMUS]] | | |[[MACSIMUS]] |
| |[[molecular dynamics]] | | | |
| |'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | | |'''MAC'''romolecule '''SIMU'''lation '''S'''oftware |
| |free | | | |
| |-
| |
| |[[MAPS]]
| |
| |simulation front-end, various
| |
| |'''Ma'''terials '''P'''rocesses and '''S'''imulations
| |
| |commercial
| |
| |- | | |- |
| |[[Materials Studio]] | | |[[Materials Studio]] |
| |various
| |
| | | | | |
| |commercial | | | |
| | | |
| |- | | |- |
| |[[MCCCS Towhee]] | | |[[MCCCS Towhee]] |
| |[[Monte Carlo]]
| |
| | | | | |
| |free source | | | |
| | | |
| |- | | |- |
| |[[MCPRO]] | | |[[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]] | | |[[Moldy]] |
| |[[molecular dynamics]] | | |[[Molecular dynamics]] |
| | | |
| | | | | |
| |free
| |
| |- | | |- |
| |[[Molecular Workbench]] | | |[[Molecular Workbench]] |
| | | | | |
| |Interactive simulations | | |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]] | | |[[Moscito]] |
| |[[molecular dynamics]] | | |[[molecular dynamics]] |
| | | | | |
| |free (General Public License) | | | |
| |-
| |
| |[[ms2]]
| |
| |[[Molecular dynamics]], [[Monte Carlo]], [[Green-Kubo relations | Green-Kubo]] formalism
| |
| |various classical ensembles
| |
| |CPC Program Library
| |
| |- | | |- |
| |[[Music]] | | |[[Music]] |
| | | | | |
| |'''Mu'''ltipurpose '''Si'''mulation '''C'''ode | | |'''Mu'''ltipurpose '''Si'''mulation '''C'''ode |
| |free (General Public License) | | | |
| |- | | |- |
| |[[NAMD]] | | |[[NAMD]] |
| |[[molecular dynamics]] | | |[[molecular dynamics]] |
| | | | | |
| |free | | | |
| |- | | |- |
| |[[NWChem]] | | |[[NWChem]] |
| | | | | |
| |Computational chemistry | | |Computational chemistry |
| |free
| |
| |-
| |
| |[[OCCAM]]
| |
| |[[molecular dynamics]]
| |
| | | | | |
| |free
| |
| |- | | |- |
| |[[OpenMD]] | | |[[ORAC]] |
| |[[molecular dynamics]] | | |[[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]] | | |[[PINY_MD]] |
| |[[molecular dynamics]] | | |[[molecular dynamics]] |
| | | | | |
| |free | | | |
| |- | | |- |
| |[[Protein Explorer]] | | |[[Protein Explorer]] |
| |visualisation | | | |
| |molecular graphics | | |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]] | | |[[RasMol]] |
| |visualisation | | | |
| |molecular graphics | | |molecular graphics |
| |free source
| |
| |-
| |
| |[[RedMD]]
| |
| |[[molecular dynamics]]
| |
| |'''Red'''uced '''M'''olecular '''D'''ynamics
| |
| |free, Open source
| |
| |-
| |
| |[[SageMD]]
| |
| |simulation front and back end
| |
| |
| |
| | | | | |
| |- | | |- |
| |[[SIESTA]] | | |[[SIESTA]] |
| |[[ab initio molecular dynamics]] | | | |
| |'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms | | |'''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]] | | |[[SYBYL]] |
| |various
| |
| | | | | |
| |commercial
| |
| |-
| |
| |[[Tesla Bio Workbench]]
| |
| | | | | |
| |GPU computing
| |
| | | | | |
| |- | | |- |
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| |Software tools for molecular design | | |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]] | | |[[VASP]] |
| |[[ab initio molecular dynamics]] | | |[[Ab initio molecular dynamics]] |
| | | | | |
| | | | | |
| |- | | |- |
| |[[VMD]] | | |[[VMD]] |
| |visualisation | | | |
| |Molecular dynamics visualisation in 3-dimensions | | |Molecular dynamics visualisation in 3-dimensions |
| |free | | | |
| |- | | |- |
| |[[WIEN2K]] | | |[[WIEN2K]] |
| | | | | |
| |Electronic structure calculation in solids | | |Electronic structure calculation in solids |
| |commercial | | | |
| |- | | |- |
| |[[XCrysDen]] | | |[[XCrysDen]] |
| |visualisation | | | |
| |Crystalline and molecular structure visualisation | | |Crystalline and molecular structure visualisation |
| |free (General Public License)
| |
| |-
| |
| |[[XMakemol]] [http://www.nongnu.org/xmakemol/]
| |
| |visualisation
| |
| | | | | |
| |free
| |
| |- | | |- |
| |[[X-PLOR]] | | |[[X-PLOR]] |
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| |[[YASARA]] | | |[[YASARA]] |
| | | | | |
| |
| |
| |free & commercial
| |
| |-
| |
| |[[YASP]] [http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html]
| |
| |[[molecular dynamics]]
| |
| | | | | |
| | | | | |
| |} | | |} |
|
| |
|
| <references/>
| |
| [[category: Materials modelling and computer simulation codes]] | | [[category: Materials modelling and computer simulation codes]] |