Editing Materials modelling and computer simulation codes

Jump to navigation Jump to search
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.

The edit can be undone. Please check the comparison below to verify that this is what you want to do, and then publish the changes below to finish undoing the edit.

Latest revision Your text
Line 1: Line 1:
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 (to change sort criteria click on the square icon next to the column title)  of software for use in materials modelling and computer simulation.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
|-
Line 6: Line 6:
|[[Abalone]]
|[[Abalone]]
|[[molecular dynamics]], visualisation
|[[molecular dynamics]], visualisation
|biopolymers
|biopolimers
|Free
|commercial
|-  
|-  
|[[ACEMD]]
|[[ACEMD]]
|[[molecular dynamics]]
|[[molecular dynamics]]
|biopolymers
|biopolimers
|commercial
|free/commercial
|-
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
Line 18: Line 18:
|Assisted Model Building with Energy Refinement
|Assisted Model Building with Energy Refinement
|commercial
|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]]
Line 38: Line 23:
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|commercial
|-
|[[BRAHMS]]
|[[molecular dynamics]]
|'''B'''iomembrane '''R'''educed-'''A'''pproac'''H''' '''M'''olecular '''S'''imulator
|in development
|-
|-
|[[CASTEP]]  
|[[CASTEP]]  
Line 68: Line 48:
|Computational chemistry
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|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]]
Line 93: Line 63:
|Molecular simulation package
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|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]]
|[[ESPResSo]]
Line 118: Line 73:
|development environment
|development environment
|free
|free
|-
|[[FOCUS]]
|molecular dynamics analysis
|
|
|-
|[[GALAMOST]]
|[[molecular dynamics]]
|GPU-Accelerated Large-Scale Molecular Simulation Toolkit
|free (GNU license)
|-
|-
|[[Gaussian]]
|[[Gaussian]]
Line 138: Line 83:
|molecular dynamics visualisation  
|molecular dynamics visualisation  
|free (GNU license)
|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]]
Line 157: Line 92:
|[[molecular dynamics]]
|[[molecular dynamics]]
|biomolecular systems
|biomolecular systems
|free for academics, fee otherwise
|-
|[[GULP]]
|[[lattice dynamics]]
|'''G'''eneral '''U'''tility '''L'''attice '''P'''rogram
|free for academics, fee otherwise
|free for academics, fee otherwise
|-
|-
Line 173: Line 103:
|
|
|
|
|-
|[[iRASPA]]
|visualisation
|
|free (Mac App Store)
|-  
|-  
|[[Jmol]]
|[[Jmol]]
|visualisation
|molecular visualisation
|
|
|free
|free
Line 193: Line 118:
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|free
|-
|[[MAPS]]
|simulation front-end, various
|'''Ma'''terials '''P'''rocesses and '''S'''imulations
|commercial
|-
|-
|[[Materials Studio]]
|[[Materials Studio]]
Line 218: Line 138:
|molecular dynamics of mixtures
|molecular dynamics of mixtures
|free (GNU license)  
|free (GNU license)  
|-
|[[MOIL]]
|[[molecular dynamics]]
|
|Open Source
|-
|-
|[[Moldy]]  
|[[Moldy]]  
Line 233: Line 148:
|Interactive simulations
|Interactive simulations
|free, Open Source
|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]]
Line 243: Line 153:
|
|
|free (General Public License)
|free (General Public License)
|-
|[[ms2]]
|[[Molecular dynamics]], [[Monte Carlo]], [[Green-Kubo relations | Green-Kubo]] formalism
|various classical ensembles
|CPC Program Library
|-
|-
|[[Music]]
|[[Music]]
Line 262: Line 167:
|
|
|Computational chemistry
|Computational chemistry
|free
|-
|[[OCCAM]]
|[[molecular dynamics]]
|
|free
|free
|-
|-
Line 278: Line 178:
|
|
|free
|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]]
|[[Packmol]]
Line 288: Line 183:
|creates an initial configuration for use in simulations
|creates an initial configuration for use in simulations
|free (GNU license)  
|free (GNU license)  
|-
|[[Peacemaker]]
|statistical thermodynamics
|Quantum cluster equilibrium calculations.
|free (GNU GPL v3)
|-
|-
|[[PINY_MD]]  
|[[PINY_MD]]  
Line 304: Line 194:
|free
|free
|-
|-
|[[PyMol]] [http://www.pymol.org/]
|[[Q molecular dynamics program | Q]] ([http://xray.bmc.uu.se/~aqwww/q/ link])
|visualisation
|molecular graphics
|commercial (academic: free)
|-
|[[Q]] [http://xray.bmc.uu.se/~aqwww/q/]
|[[molecular dynamics]]
|[[molecular dynamics]]
|[[Helmholtz energy function |free energy]] calculations in [[Biological systems | biomolecular systems]]
|[[Helmholtz energy function |free energy]] calculations in [[Biological systems | biomolecular systems]]
|free with [http://xray.bmc.uu.se/~aqwww/q/q_license.pdf licence]
|free with [http://xray.bmc.uu.se/~aqwww/q/q_license.pdf licence]
|-
|[[QMGA]]
|visualisation
|molecular graphics
|free source
|-
|-
|[[RasMol]]  
|[[RasMol]]  
Line 323: Line 203:
|molecular graphics
|molecular graphics
|free source
|free source
|-
|[[RedMD]]
|[[molecular dynamics]]
|'''Red'''uced '''M'''olecular '''D'''ynamics
|free, Open source
|-
|-
|[[SageMD]]
|[[SageMD]]
|simulation front and back end
|simulation fornt and back end
|
|
|
|
Line 343: Line 218:
|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins
|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins
|free (General Public License) with restrictions
|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]]
Line 363: Line 233:
|Software tools for molecular design
|Software tools for molecular design
|free source
|free source
|-
|[[toyMD]]
|[[molecular dynamics]]
|
|free (non-commercial)
|-
|[[UHBD]]
|[[brownian dynamics]]
|'''U'''niversity of '''H'''ouston '''B'''rownian '''D'''ynamics
|license required
|-
|-
|[[VASP]]
|[[VASP]]
Line 393: Line 253:
|Crystalline and molecular structure visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|free (General Public License)
|-
|[[XMakemol]] [http://www.nongnu.org/xmakemol/]
|visualisation
|
|free
|-
|-
|[[X-PLOR]]
|[[X-PLOR]]
Line 409: Line 264:
|free & commercial
|free & commercial
|-
|-
|[[YASP]] [http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html]
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP]
|[[molecular dynamics]]
|[[molecular dynamics]]
|
|
Line 415: Line 270:
|}
|}


<references/>
[[category: Materials modelling and computer simulation codes]]
[[category: Materials modelling and computer simulation codes]]
Please note that all contributions to SklogWiki are considered to be released under the Creative Commons Attribution Non-Commercial Share Alike (see SklogWiki:Copyrights for details). If you do not want your writing to be edited mercilessly and redistributed at will, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource. Do not submit copyrighted work without permission!

To edit this page, please answer the question that appears below (more info):

Cancel Editing help (opens in new window)
Retrieved from "http://www.sklogwiki.org/SklogWiki/index.php/Materials_modelling_and_computer_simulation_codes"