Editing Materials modelling and computer simulation codes
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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 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 <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 | ||
| | |biopolimers | ||
| | |commercial | ||
|- | |- | ||
|[[ACEMD]] | |[[ACEMD]] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
| | |biopolimers | ||
|commercial | |free/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 | ||
|- | |- | ||
|[[BOSS]] | |[[BOSS]] | ||
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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] | ||
|- | |- | ||
|[[DiMol2D]] | |[[DiMol2D]] | ||
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|Molecular simulation package | |Molecular simulation package | ||
|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] | ||
|- | |- | ||
|[[EGO VIII]] | |[[EGO VIII]] | ||
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|development environment | |development environment | ||
|free | |free | ||
|- | |- | ||
|[[Gaussian]] | |[[Gaussian]] | ||
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|molecular dynamics visualisation | |molecular dynamics visualisation | ||
|free (GNU license) | |free (GNU license) | ||
|- | |- | ||
|[[GROMACS]] | |[[GROMACS]] | ||
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|[[molecular dynamics]] | |[[molecular dynamics]] | ||
|biomolecular systems | |biomolecular systems | ||
|free for academics, fee otherwise | |free for academics, fee otherwise | ||
|- | |- | ||
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| | | | ||
|- | |- | ||
|[[Jmol]] | |[[Jmol]] | ||
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|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | |'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | ||
|free | |free | ||
|- | |- | ||
|[[Materials Studio]] | |[[Materials Studio]] | ||
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|molecular dynamics of mixtures | |molecular dynamics of mixtures | ||
|free (GNU license) | |free (GNU license) | ||
|- | |- | ||
|[[Moldy]] | |[[Moldy]] | ||
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|Interactive simulations | |Interactive simulations | ||
|free, Open Source | |free, Open Source | ||
|- | |- | ||
|[[Moscito]] | |[[Moscito]] | ||
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| | | | ||
|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[[Music]] | |[[Music]] | ||
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|Computational chemistry | |Computational chemistry | ||
|free | |free | ||
|- | |- | ||
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| | | | ||
|free | |free | ||
|- | |- | ||
|[[Packmol]] | |[[Packmol]] | ||
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|creates an initial configuration for use in simulations | |creates an initial configuration for use in simulations | ||
|free (GNU license) | |free (GNU license) | ||
|- | |- | ||
|[[PINY_MD]] | |[[PINY_MD]] | ||
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|free | |free | ||
|- | |- | ||
|[[ | |[[Q molecular dynamics program | Q]] ([http://xray.bmc.uu.se/~aqwww/q/ link]) | ||
| | |||
|[[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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|[[SageMD]] | |[[SageMD]] | ||
|simulation | |simulation fornt and back end | ||
| | | | ||
| | | | ||
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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 | ||
|- | |- | ||
|[[SYBYL]] | |[[SYBYL]] | ||
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|Software tools for molecular design | |Software tools for molecular design | ||
|free source | |free source | ||
|- | |- | ||
|[[VASP]] | |[[VASP]] | ||
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|Crystalline and molecular structure visualisation | |Crystalline and molecular structure visualisation | ||
|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[[X-PLOR]] | |[[X-PLOR]] | ||
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|free & commercial | |free & commercial | ||
|- | |- | ||
| | |[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
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