Materials modelling and computer simulation codes: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
Carl McBride (talk | contribs) m (Slight tidy) |
||
| Line 159: | Line 159: | ||
|free | |free | ||
|- | |- | ||
|[http://www.scienomics.com/products/molecular-modeling-platform | |[[MAPS]] [http://www.scienomics.com/products/molecular-modeling-platform] | ||
| | |simulation front-end | ||
| | |'''Ma'''terials '''P'''rocesses and '''S'''imulations | ||
|commercial | |commercial | ||
|- | |- | ||
| Line 254: | Line 254: | ||
|free | |free | ||
|- | |- | ||
|[http://www.pymol.org/ | |[[PyMol]] [http://www.pymol.org/] | ||
|visualisation | |visualisation | ||
|molecular graphics | |molecular graphics | ||
|commercial (academic: free) | |commercial (academic: free) | ||
|- | |- | ||
|[http://xray.bmc.uu.se/~aqwww/q/ | |[[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]] | ||
| Line 334: | Line 334: | ||
|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[http://www.nongnu.org/xmakemol/ | |[[XMakemol]] [http://www.nongnu.org/xmakemol/] | ||
|visualisation | |visualisation | ||
| | | | ||
| Line 349: | Line 349: | ||
|free & commercial | |free & commercial | ||
|- | |- | ||
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html | |[[YASP]] [http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
| | | | ||
Revision as of 11:21, 22 June 2012
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 program | Focus | Notes | License |
|---|---|---|---|
| Abalone | molecular dynamics, visualisation | biopolimers | Free |
| ACEMD | molecular dynamics | biopolimers | free/commercial |
| AMBER | molecular dynamics | Assisted Model Building with Energy Refinement | commercial |
| 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 | |
| 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 | ||
| Gaussian | electronic structure | Computational chemistry | commercial |
| gdpc | visualisation | molecular dynamics visualisation | free (GNU license) |
| 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 | ||
| Jmol | visualisation | free | |
| LAMMPS | molecular dynamics | free source (GNU license) | |
| MACSIMUS | molecular dynamics | MACromolecule SIMUlation Software | free |
| MAPS [1] | simulation front-end | 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 | |
| Moscito | molecular dynamics | free (General Public License) | |
| 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 | |
| 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 [2] | visualisation | molecular graphics | commercial (academic: free) |
| Q [3] | 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 |
| SYBYL | various | commercial | |
| Tesla Bio Workbench | GPU computing | ||
| TINKER | Software tools for molecular design | free source | |
| 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 [4] | visualisation | free | |
| X-PLOR | Computational structural biology | ||
| YASARA | free & commercial | ||
| YASP [5] | molecular dynamics |