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, 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 |