Materials modelling and computer simulation codes

2016-11-21T08:26:43Z

Scienomics:

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 and computer simulation. 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
|biopolimers
|Free
|-
|[[ACEMD]]
|[[molecular dynamics]]
|biopolimers
|commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[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
|
|
|-
|[[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]]
|
|
|-
|[[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)
|-
|[[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
|-
|[[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/>
[[category: Materials modelling and computer simulation codes]]

MAPS

2016-11-21T08:25:16Z

Scienomics:

Materials and Process Simulation, [http://www.scienomics.com/software/ MAPS], platform is a multi-scale, multi-paradigm, extensible platform that allows engineers and scientists to BUILD realistic models of all types of materials, SIMULATE various properties and processes using world-leading simulation engines and ANALYZE for key properties to predict and screen materials behavior under different conditions.

[http://www.scienomics.com/build/ BUILD]
The builders within the MAPS platform provide graphical interfaces for model building of any type of materials.

[http://www.scienomics.com/simulate/ SIMULATE]
The MAPS platform offers plugins and Graphical User Interfaces to proprietary and third party simulation engines in Materials Science. MAPS users can quickly setup calculations with the most advanced codes in the QUANTUM, CLASSICAL & MESOSCALE, THERMODYNAMICS and INFORMATICS domains.

[http://www.scienomics.com/analyze/ ANALYZE]
MAPS provides a powerful analysis toolkit for all properties generated by the supported simulation engines. In addition MAPS offers a collection of Python based tools that extend its standard analysis capability.

[http://www.scienomics.com/infrastructure/ INFRASTRUCTURE]
MAPS architecture allows fast development and deployment of new and extension of existing functionality.

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

MAPS

2016-11-21T08:24:12Z

Scienomics: Creation of Scienomics' MAPS platform

Materials and Process Simulation, [http://www.scienomics.com/software/ MAPS], platform is a multi-scale, multi-paradigm, extensible platform that allows engineers and scientists to BUILD realistic models of all types of materials, SIMULATE various properties and processes using world-leading simulation engines and ANALYZE for key properties to predict and screen materials behavior under different conditions.

[http://www.scienomics.com/build/ BUILD]
The builders within the MAPS platform provide graphical interfaces for model building of any type of materials.

[http://www.scienomics.com/simulate/ SIMULATE]
The MAPS platform offers plugins and Graphical User Interfaces to proprietary and third party simulation engines in Materials Science. MAPS users can quickly setup calculations with the most advanced codes in the QUANTUM, CLASSICAL & MESOSCALE, THERMODYNAMICS and INFORMATICS domains.

[http://www.scienomics.com/analyze/ ANALYZE]
MAPS provides a powerful analysis toolkit for all properties generated by the supported simulation engines. In addition MAPS offers a collection of Python based tools that extend its standard analysis capability.

[http://www.scienomics.com/infrastructure/INFRASTRUCTURE]
MAPS architecture allows fast development and deployment of new and extension of existing functionality.

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

SklogWiki - User contributions [en]

Materials modelling and computer simulation codes

MAPS

MAPS