Materials modelling and computer simulation codes: Difference between revisions

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*[[DL_POLY: Molecular Simulation Package]]
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>.
*[[LAMMPS: Molecular Dynamics Simulator]]
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
*[[DiMol2D: Molecular Dynamics Visualization]]
|-
*[[VMD: Molecular Dynamics Visualization in 3D]]
! Computer program !! Focus !! class="unsortable" | Notes !! License 
*[[XCrysDen: Crystalline and molecular structure visualisation]]
|-
*[[Gaussian]]: Computational Chemistry
|[[Abalone]]
*[[Assisted Model Building with Energy Refinement (AMBER)]]
|[[molecular dynamics]], visualisation
*[[NAMD]]: Classical MD
|biopolymers
*[[CHARMM]]: Chemistry at HARvard Molecular Mechanics
|Free
*[[GROMACS]]: Classical MD
|-
*[[X-PLOR]]: Computational structural biology
|[[ACEMD]]
*[[VASP]]: Ab initio MD
|[[molecular dynamics]]
*[[CPMD]]: Carr-Parrinello MD
|biopolymers
*[[WIEN2K]]: Electronic structure calculation in solids
|commercial
*[[NWCHEM]]: Computational Chemistry
|-
*[[Dalton]]: Computational Chemistry
|[[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/>
[[category: Materials modelling and computer simulation codes]]

Latest revision as of 07:53, 5 June 2020

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 [1].

Computer program Focus Notes License
Abalone molecular dynamics, visualisation biopolymers Free
ACEMD molecular dynamics biopolymers commercial
AMBER molecular dynamics Assisted Model Building with Energy Refinement commercial
Assemble! configuration preparation preparation of molecular dynamics simulations of polymeric systems Computer Physics Communications library
AVOGADRO [1] visualisation molecule editor and visualizer free
BD_BOX Brownian dynamics scalable (CPU/GPU) Brownian dynamics package for UNIX/LINUX platforms GNU Public License
BOSS Biochemical and Organic Simulation System commercial
BRAHMS molecular dynamics Biomembrane Reduced-ApproacH Molecular Simulator in development
CASTEP density-functional theory commercial (free in United Kingdom)
CCP5 Program Library various program library free to academics
CHARMM Chemistry at HARvard Molecular Mechanics commercial
CPMD ab initio molecular dynamics Carr-Parrinello Molecular Dynamics free with license
Dalton Computational chemistry free with license
DeePMD-kit [2] 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 academic license
DL_POLY molecular dynamics Molecular simulation package free source with academic license
DynamO molecular dynamics Event-driven molecular dynamics free source
EGO VIII molecular dynamics free
ENCAD molecular dynamics Energy Calculation and Dynamics
ESPResSo molecular dynamics Extensible Simulation Package for Research on Soft 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 [3] Binary phase diagrams Global Phase Equilibrium Calculations free
GPIUTMD molecular dynamics Graphical Processors at Isfahan University of Technology for Many-particle Dynamics not free, commercial
GROMACS molecular dynamics free source
GROMOS molecular dynamics biomolecular systems free for academics, fee otherwise
GULP lattice dynamics General Utility Lattice Program free for academics, fee otherwise
HOOMD molecular dynamics Highly Optimized Object Oriented Molecular Dynamics. 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 MACromolecule SIMUlation Software free
MAPS simulation front-end, various Materials Processes and Simulations 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
MoRiBS-PIMC 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 formalism various classical ensembles CPC Program Library
Music Multipurpose Simulation Code 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
oxDNA Monte Carlo and brownian dynamics simulation code that implements coarse-grained models for DNA and RNA [4] 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 [5] visualisation molecular graphics commercial (academic: free)
Q [6] molecular dynamics free energy calculations in biomolecular systems free with licence
QMGA visualisation molecular graphics free source
RasMol visualisation molecular graphics free source
RedMD molecular dynamics Reduced Molecular Dynamics free, Open source
SageMD simulation front and back end
SIESTA ab initio molecular dynamics Spanish Initiative for Electronic Simulations with Thousands of Atoms free for academics, fee otherwise
SMMP Monte Carlo Simple Molecular Mechanics for Proteins free (General Public License) with restrictions
SSAGES Ensemble simulations Software Suite for Advanced Generalized Ensemble Simulations 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 University of Houston Brownian Dynamics 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 [7] visualisation free
X-PLOR Computational structural biology
YASARA free & commercial
YASP [8] molecular dynamics
  1. ↑ Wilfred F. van Gunsteren, and Alan E. Mark "Validation of molecular dynamics simulation", Journal of Chemical Physics 108 pp. 6109-6116 (1998)
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