List of nucleic acid simulation software

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This is a list of computer programs that are used for nucleic acids simulations.

Min - Optimization, MD - Molecular dynamics, MC - Monte Carlo, REM - Replica exchange method,

Crt - Cartesian coordinates. Int - Internal coordinates Exp - Explicit water. Imp - Implicit water.

Lig - Ligands interactions. HA - Hardware accelerated.

Name	View 3D	Model Build	Min	MD	MC	REM	Crt	Int	Exp	Imp	Lig	HA	Comments	License	Homepage
Abalone	+	+	+	+	+	+	+		+	+	+	+	DNA, proteins, ligands	Free	Agile Molecule
AMBER ^[1]		+	+	+		+	+		+	+	+		AMBER Force Field	Commercial	ambermd.org
Ascalaph Designer	+	+	+	+			+		+	+	+		AMBER	GPL	biomolecular-modeling.com
CHARMM		+	+	+	+		+		+	+	+		CHARMM Force Field	Commercial	charmm.org
ICM^[2]	+	+	+		+			+		+			Global optimization	Commercial	Molsoft
JUMNA ^[3]		+	+					+		+				Commercial
MDynaMix ^[4]	+	+		+			+		+		+		Common MD	GPL	Stockholm University
MOE	+	+	+	+			+		+		+		Molecular Operating Environment	Commercial	Chemical Computing Group
NAB ^[5]		+											Nucleic Acid Builder	GPL	New Jersey University
NAMD	+		+	+			+		+		+	+	NAnoscale Molecular Dynamics	Free	University of Illinois

[edit] See also

^ Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Jr., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W. and Kollman P.A. (1995). "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules". J. Am. Chem. Soc. 117: 5179–5197. doi:10.1021/ja00124a002.
^ Abagyan R.A., Totrov M.M. and Kuznetsov D.A. (1994). "Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation". J. Comp. Chem. 15: 488–506. doi:10.1002/jcc.540150503.
^ Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comp. Phys. Commun. 91: 135–158. doi:10.1016/0010-4655(95)00046-I.
^ A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications 128: 565–589. doi:10.1016/S0010-4655(99)00529-9.
^ Macke T. and Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.

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