Comparison of nucleic acid simulation software
This is a list of notable computer programs that are used for nucleic acids simulations.
| Name | View 3D | Model build | Min | MD | MC | REM | Crt | Int | Exp | Imp | Lig | GPU | Comments | License | Website |
| Abalone | DNA, proteins, ligands | ||||||||||||||
| AMBER | AMBER force field | ||||||||||||||
| Ascalaph Designer | AMBER | , GPL | |||||||||||||
| CHARMM | CHARMM force field | ||||||||||||||
| CP2K | , GPL | ||||||||||||||
| Forecaster | Small molecule docking to nucleic acids with water placement | Free for academia, Proprietary | |||||||||||||
| ICM | Global optimization | ||||||||||||||
| JUMNA | |||||||||||||||
| MDynaMix | Common MD | , GPL | |||||||||||||
| Molecular Operating Environment | |||||||||||||||
| Nucleic Acid Builder | Generates models for unusual DNA, RNA | , GPL | |||||||||||||
| NAnoscale Molecular Dynamics | Fast, parallel MD, CUDA | ||||||||||||||
| oxDNA | Coarse-grained models of DNA, RNA | , GPL | |||||||||||||
| QRNAS | High resolution refinement of models of RNA, DNA and hybrids using AMBER force field. | , GPL | |||||||||||||
| SimRNA | Coarse grained modeling of RNA | Free for Academic, Proprietary | |||||||||||||
| SimRNAweb | Coarse grained modeling of RNA | Free | |||||||||||||
| YASARA | Interactive simulations |