Sunday, February 15, 2015

SklogWiki: Materials modelling and computer simulation codes

Materials modelling and computer simulation codes

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 [1].
Computer programFocusNotesLicense
Abalonemolecular dynamics, visualisationbiopolimersFree
ACEMDmolecular dynamicsbiopolimerscommercial
AMBERmolecular dynamicsAssisted Model Building with Energy Refinementcommercial
AVOGADRO [1]visualisationmolecule editor and visualizerfree
BD_BOXBrownian dynamicsscalable (CPU/GPU) Brownian dynamics package for UNIX/LINUX platformsGNU Public License
BOSSBiochemical and Organic Simulation Systemcommercial
BRAHMSmolecular dynamicsBiomembrane Reduced-ApproacH Molecular Simulatorin development
CASTEPdensity-functional theorycommercial (free in United Kingdom)
CCP5 Program Libraryvariousprogram libraryfree to academics
CHARMMChemistry at HARvard Molecular Mechanicscommercial
CPMDab initio molecular dynamicsCarr-Parrinello Molecular Dynamicsfree with license
DaltonComputational chemistryfree with license
DiMol2Dmolecular dynamicsMolecular dynamics visualizationfree executable
DL_MESOdissipative particle dynamicsMesoscale simulation packagefree source with academic license
DL_POLYmolecular dynamicsMolecular simulation packagefree source with academic license
DYNAMOmolecular dynamicsEvent-driven molecular dynamicsfree source
EGO VIIImolecular dynamicsfree
ENCADmolecular dynamicsEnergy Calculation and Dynamics
ESPResSomolecular dynamicsExtensible Simulation Package for Research on Soft matterfree
Etomicadevelopment environmentfree
FOCUSmolecular dynamics analysis
Gaussianelectronic structureComputational chemistrycommercial
gdpcvisualisationmolecular dynamics visualisationfree (GNU license)
GPEC [2]Binary phase diagramsGlobal Phase Equilibrium Calculationsfree
GPIUTMDmolecular dynamicsGraphical Processors at Isfahan University of Technology for Many-particle Dynamicsnot free, commercial
GROMACSmolecular dynamicsfree source
GROMOSmolecular dynamicsbiomolecular systemsfree for academics, fee otherwise
GULPlattice dynamicsGeneral Utility Lattice Programfree for academics, fee otherwise
HOOMDmolecular dynamicsHighly Optimized Object Oriented Molecular, Open Source
IMDmolecular dynamics
LAMMPSmolecular dynamicsfree source (GNU license)
MACSIMUSmolecular dynamicsMACromolecule SIMUlation Softwarefree
MAPS [3]simulation front-endMaterials Processes and Simulationscommercial
Materials Studiovariouscommercial
MCCCS TowheeMonte Carlofree source
MCPROMonte Carlopeptides, proteins, and nucleic acids in solutioncommercial
MDynaMixmolecular dynamicsmolecular dynamics of mixturesfree (GNU license)
MOILmolecular dynamicsOpen Source
Moldymolecular dynamicsfree
Molecular WorkbenchInteractive simulationsfree, Open Source
Moscitomolecular dynamicsfree (General Public License)
MusicMultipurpose Simulation Codefree (General Public License)
NAMDmolecular dynamicsfree
NWChemComputational chemistryfree
OCCAMmolecular dynamicsfree
OpenMDmolecular dynamicsfree - Open Source
ORACmolecular dynamicsfree
oxDNAMonte Carlo and brownian dynamicssimulation code that implements coarse-grained models for DNA and RNA [4]free (GNU General Public License)
Packmolmolecular dynamicscreates an initial configuration for use in simulationsfree (GNU license)
Peacemakerstatistical thermodynamicsQuantum cluster equilibrium (GNU GPL v3)
PINY_MDmolecular dynamicsfree
Protein Explorervisualisationmolecular graphicsfree
PyMol [5]visualisationmolecular graphicscommercial (academic: free)
Q [6]molecular dynamicsfree energy calculations in biomolecular systemsfree with licence
QMGAvisualisationmolecular graphicsfree source
RasMolvisualisationmolecular graphicsfree source
RedMDmolecular dynamicsReduced Molecular Dynamicsfree, Open source
SageMDsimulation front and back end
SIESTAab initio molecular dynamicsSpanish Initiative for Electronic Simulations with Thousands of Atomsfree for academics, fee otherwise
SMMPMonte CarloSimple Molecular Mechanics for Proteinsfree (General Public License) with restrictions
Tesla Bio WorkbenchGPU computing
TINKERSoftware tools for molecular designfree source
toyMDmolecular dynamicsfree (non-commercial)
UHBDbrownian dynamicsUniversity of Houston Brownian Dynamicslicense required
VASPab initio molecular dynamics
VMDvisualisationMolecular dynamics visualisation in 3-dimensionsfree
WIEN2KElectronic structure calculation in solidscommercial
XCrysDenvisualisationCrystalline and molecular structure visualisationfree (General Public License)
XMakemol [7]visualisationfree
X-PLORComputational structural biology
YASARAfree & commercial
YASP [8]molecular dynamics
  1. Jump up 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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