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 | ||
|- | |- | ||
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]] | |[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]] | ||
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|Assisted Model Building with Energy Refinement | |Assisted Model Building with Energy Refinement | ||
|commercial | |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]] | |[[BD_BOX]] | ||
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|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]] | |||
|[[molecular dynamics]] | |||
| | |||
|commercial, free for academics | |||
|- | |- | ||
|[[DiMol2D]] | |[[DiMol2D]] | ||
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|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license] | |free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license] | ||
|- | |- | ||
|[[ | |[[DynamO]] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
|[[Event-driven molecular dynamics]] | |[[Event-driven molecular dynamics]] | ||
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| | | | ||
| | | | ||
|- | |||
|[[GALAMOST]] | |||
|[[molecular dynamics]] | |||
|GPU-Accelerated Large-Scale Molecular Simulation Toolkit | |||
|free (GNU license) | |||
|- | |- | ||
|[[Gaussian]] | |[[Gaussian]] | ||
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|molecular dynamics visualisation | |molecular dynamics visualisation | ||
|free (GNU license) | |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]] | |[[GROMACS]] | ||
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| | | | ||
| | | | ||
|- | |||
|[[iRASPA]] | |||
|visualisation | |||
| | |||
|free (Mac App Store) | |||
|- | |- | ||
|[[Jmol]] | |[[Jmol]] | ||
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|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | |'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | ||
|free | |free | ||
|- | |||
|[[MAPS]] | |||
|simulation front-end, various | |||
|'''Ma'''terials '''P'''rocesses and '''S'''imulations | |||
|commercial | |||
|- | |- | ||
|[[Materials Studio]] | |[[Materials Studio]] | ||
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|Interactive simulations | |Interactive simulations | ||
|free, Open Source | |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]] | |[[Moscito]] | ||
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| | | | ||
|free (General Public License) | |free (General Public License) | ||
|- | |||
|[[ms2]] | |||
|[[Molecular dynamics]], [[Monte Carlo]], [[Green-Kubo relations | Green-Kubo]] formalism | |||
|various classical ensembles | |||
|CPC Program Library | |||
|- | |- | ||
|[[Music]] | |[[Music]] | ||
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| | | | ||
|Computational chemistry | |Computational chemistry | ||
|free | |||
|- | |||
|[[OCCAM]] | |||
|[[molecular dynamics]] | |||
| | |||
|free | |free | ||
|- | |- | ||
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| | | | ||
|free | |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]] | |[[Packmol]] | ||
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|free | |free | ||
|- | |- | ||
|[http://www.pymol.org/ | |[[PyMol]] [http://www.pymol.org/] | ||
|visualisation | |visualisation | ||
|molecular graphics | |molecular graphics | ||
|commercial (academic: free) | |commercial (academic: free) | ||
|- | |- | ||
|[[ | |[[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]] | ||
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|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins | |'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins | ||
|free (General Public License) with restrictions | |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]] | |[[SYBYL]] | ||
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|Software tools for molecular design | |Software tools for molecular design | ||
|free source | |free source | ||
|- | |||
|[[toyMD]] | |||
|[[molecular dynamics]] | |||
| | |||
|free (non-commercial) | |||
|- | |- | ||
|[[UHBD]] | |[[UHBD]] | ||
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|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[http://www.nongnu.org/xmakemol/ | |[[XMakemol]] [http://www.nongnu.org/xmakemol/] | ||
|visualisation | |visualisation | ||
| | | | ||
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|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]] | ||
| | | |
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 |