Materials modelling and computer simulation codes: Difference between revisions
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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 | 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>. | ||
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0" | {| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0" | ||
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|[[Abalone]] | |[[Abalone]] | ||
|[[molecular dynamics]], visualisation | |[[molecular dynamics]], visualisation | ||
| | |biopolymers | ||
|Free | |Free | ||
|- | |- | ||
|[[ACEMD]] | |[[ACEMD]] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
| | |biopolymers | ||
|commercial | |commercial | ||
|- | |- | ||
| Line 68: | Line 68: | ||
|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]] | |[[Desmond]] | ||
| Line 118: | Line 123: | ||
| | | | ||
| | | | ||
|- | |||
|[[GALAMOST]] | |||
|[[molecular dynamics]] | |||
|GPU-Accelerated Large-Scale Molecular Simulation Toolkit | |||
|free (GNU license) | |||
|- | |- | ||
|[[Gaussian]] | |[[Gaussian]] | ||
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 |