Comparison of nucleic acid simulation software


This is a list of computer programs that are used for nucleic acids simulations.
NameView 3DModel buildMinMDMCREMCrtIntExpImpLigGPUCommentsLicenseWebsite
AbaloneDNA, proteins, ligands
AMBERAMBER force field
Ascalaph DesignerAMBER, GPL
CHARMMCHARMM force field
CP2K, GPL
Forecaster Small molecule docking to nucleic acids with water placementFree for academia, Proprietary
HyperChemsome force fields
ICMGlobal optimization
JUMNA
MDynaMixCommon MD, GPL
Molecular Operating Environment
Nucleic Acid Builder Generates models for unusual DNA, RNA, GPL
NAnoscale Molecular Dynamics Fast, parallel MD, CUDA
oxDNACoarse-grained models of DNA, RNA, GPL
QRNASHigh resolution refinement of models of RNA, DNA and hybrids using AMBER force field., GPL
SimRNACoarse grained modeling of RNAFree for Academic, Proprietary
SimRNAwebCoarse grained modeling of RNAFree
YASARAInteractive simulations