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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>.
| | ===A=== |
| {| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
| | *[[AMBER -- Assisted Model Building with Energy Refinement]] |
| |-
| | ===B=== |
| ! Computer program !! Focus !! class="unsortable" | Notes !! License
| | *[[BOSS]] |
| |-
| | ===C=== |
| |[[Abalone]]
| | *[[CASTEP]] density functional theory. |
| |[[molecular dynamics]], visualisation
| | *[[CHARMM]]: Chemistry at HARvard Molecular Mechanics |
| |biopolymers
| | *[[CPMD]]: Carr-Parrinello MD |
| |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]
| |
| |-
| |
| |[[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]]
| |
| |[[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]]
| |
| |
| |
| |
| |
| |}
| |
|
| |
|
| <references/>
| | ===D=== |
| [[category: Materials modelling and computer simulation codes]] | | *[[Dalton]]: Computational Chemistry |
| | *[[DiMol2D]]: Molecular Dynamics Visualization |
| | *[[DL_POLY]]: Molecular Simulation Package |
| | ===G=== |
| | *[[Gaussian]]: Computational Chemistry |
| | *[[GROMACS]]: Classical MD |
| | *[[GROMOS]] |
| | |
| | ===L=== |
| | *[[LAMMPS]]: Molecular Dynamics Simulator |
| | ===M=== |
| | *[[Materials Studio]] |
| | *[[MCPRO]] |
| | *[[Moldy]] a general-purpose molecular dynamics simulation program. |
| | *[[Molecular Workbench]] Interactive simulations |
| | |
| | ===N=== |
| | *[[NAMD]]: Classical MD |
| | *[[NWChem]]: Computational Chemistry |
| | |
| | ===T=== |
| | *[[TINKER]]: Software Tools for Molecular Design |
| | ===V=== |
| | *[[VASP]]: Ab initio MD |
| | *[[VMD]]: Molecular Dynamics Visualization in 3D |
| | ===W=== |
| | *[[WIEN2K]]: Electronic structure calculation in solids |
| | ===X=== |
| | *[[XCrysDen]]: Crystalline and molecular structure visualisation |
| | *[[X-PLOR]]: Computational structural biology |