Editing Materials modelling and computer simulation codes
Jump to navigation
Jump to search
The edit can be undone. Please check the comparison below to verify that this is what you want to do, and then publish the changes below to finish undoing the edit.
Latest revision | Your text | ||
Line 1: | Line 1: | ||
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" | ||
|- | |- | ||
Line 6: | Line 6: | ||
|[[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]] | ||
Line 18: | Line 18: | ||
|Assisted Model Building with Energy Refinement | |Assisted Model Building with Energy Refinement | ||
|commercial | |commercial | ||
|- | |- | ||
|[[BOSS]] | |[[BOSS]] | ||
Line 68: | Line 53: | ||
|Computational chemistry | |Computational chemistry | ||
|free with [http://www.theochem.kth.se/dalton/ license] | |free with [http://www.theochem.kth.se/dalton/ license] | ||
|- | |- | ||
|[[DiMol2D]] | |[[DiMol2D]] | ||
Line 93: | Line 68: | ||
|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] | ||
|- | |- | ||
|[[ESPResSo]] | |[[ESPResSo]] | ||
Line 118: | Line 78: | ||
|development environment | |development environment | ||
|free | |free | ||
|- | |- | ||
|[[Gaussian]] | |[[Gaussian]] | ||
Line 138: | Line 88: | ||
|molecular dynamics visualisation | |molecular dynamics visualisation | ||
|free (GNU license) | |free (GNU license) | ||
|- | |- | ||
|[[GROMACS]] | |[[GROMACS]] | ||
Line 157: | Line 97: | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
|biomolecular systems | |biomolecular systems | ||
|free for academics, fee otherwise | |free for academics, fee otherwise | ||
|- | |- | ||
Line 173: | Line 108: | ||
| | | | ||
| | | | ||
|- | |- | ||
|[[Jmol]] | |[[Jmol]] | ||
Line 193: | Line 123: | ||
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | |'''MAC'''romolecule '''SIMU'''lation '''S'''oftware | ||
|free | |free | ||
|- | |- | ||
|[[Materials Studio]] | |[[Materials Studio]] | ||
Line 218: | Line 143: | ||
|molecular dynamics of mixtures | |molecular dynamics of mixtures | ||
|free (GNU license) | |free (GNU license) | ||
|- | |- | ||
|[[Moldy]] | |[[Moldy]] | ||
Line 233: | Line 153: | ||
|Interactive simulations | |Interactive simulations | ||
|free, Open Source | |free, Open Source | ||
|- | |- | ||
|[[Moscito]] | |[[Moscito]] | ||
Line 243: | Line 158: | ||
| | | | ||
|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[[Music]] | |[[Music]] | ||
Line 262: | Line 172: | ||
| | | | ||
|Computational chemistry | |Computational chemistry | ||
|free | |free | ||
|- | |- | ||
Line 278: | Line 183: | ||
| | | | ||
|free | |free | ||
|- | |- | ||
|[[Packmol]] | |[[Packmol]] | ||
Line 288: | Line 188: | ||
|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]] | ||
Line 304: | Line 199: | ||
|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]] | ||
Line 330: | Line 220: | ||
|- | |- | ||
|[[SageMD]] | |[[SageMD]] | ||
|simulation | |simulation fornt and back end | ||
| | | | ||
| | | | ||
Line 343: | Line 233: | ||
|'''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]] | ||
Line 363: | Line 248: | ||
|Software tools for molecular design | |Software tools for molecular design | ||
|free source | |free source | ||
|- | |- | ||
|[[VASP]] | |[[VASP]] | ||
Line 393: | Line 268: | ||
|Crystalline and molecular structure visualisation | |Crystalline and molecular structure visualisation | ||
|free (General Public License) | |free (General Public License) | ||
|- | |- | ||
|[[X-PLOR]] | |[[X-PLOR]] | ||
Line 409: | Line 279: | ||
|free & commercial | |free & commercial | ||
|- | |- | ||
| | |[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP] | ||
|[[molecular dynamics]] | |[[molecular dynamics]] | ||
| | | |