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	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	DNA, proteins, ligands	Free
AMBER	No	Yes	Yes	Yes	No	Yes	Yes	No	Yes	Yes	Yes	Yes	AMBER force field	Proprietary
Ascalaph Designer	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	Yes	Yes	No	AMBER	Free, GPL
CHARMM	No	Yes	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	No	CHARMM force field	Proprietary
CP2K	No	No	Yes	Yes	Yes	Yes	Yes	No	Yes	No	No	Yes		Free, GPL
Forecaster (Fitted)	Yes	No	Yes	No	No	No	Yes	No	Yes	No	Yes	No	Small molecule docking to nucleic acids with water placement	Free for academia, Proprietary	2019-07-09 at the Wayback Machine
ICM	Yes	Yes	Yes	No	Yes	No	No	Yes	No	Yes	No	No	Global optimization	Proprietary
JUMNA	No	Yes	Yes	No	No	No	No	Yes	No	Yes	No	No		Proprietary
MDynaMix	Yes	Yes	No	Yes	No	No	Yes	No	Yes	No	Yes	No	Common MD	Free, GPL
Molecular Operating Environment (MOE)	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	No	Yes	No		Proprietary
Nucleic Acid Builder (NAB)	No	Yes	No	No	No	No	No	No	No	No	No	No	Generates models for unusual DNA, RNA	Free, GPL
NAnoscale Molecular Dynamics (NAMD)	Yes	No	Yes	Yes	No	No	Yes	No	Yes	No	Yes	Yes	Fast, parallel MD, CUDA	Free
oxDNA	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	Coarse-grained models of DNA, RNA	Free, GPL
QRNAS	No	No	Yes	No	No	No	Yes	No	No	Yes	No	No	High resolution refinement of models of RNA, DNA and hybrids using AMBER force field .	Free, GPL
SimRNA	Yes	Yes	No	No	Yes	Yes	Yes	Yes	No	Yes	No	No	Coarse grained modeling of RNA	Free for Academic, Proprietary
SimRNAweb	Yes	Yes	No	No	Yes	Yes	Yes	Yes	No	Yes	No	No	Coarse grained modeling of RNA	Free
YASARA	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	No	Yes	No	Interactive simulations	Proprietary

See also