List of nucleic acid simulation software

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

Min - Optimization

Optimization (mathematics)

In mathematics, computational science, or management science, mathematical optimization refers to the selection of a best element from some set of available alternatives....

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MD - Molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

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MC - Monte Carlo

Monte Carlo method

Monte Carlo methods are a class of computational algorithms that rely on repeated random sampling to compute their results. Monte Carlo methods are often used in computer simulations of physical and mathematical systems...

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REM - Replica exchange method,

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

Water model

In computational chemistry, classical water models are used for the simulation of water clusters, liquid water, and aqueous solutions with explicit solvent. These models use the approximations of molecular mechanics...

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Imp - Implicit water

Implicit solvation

Implicit solvation is a method of representing solvent as a continuous medium instead of individual “explicit” solvent molecules most often used in molecular dynamics simulations and in other applications of molecular mechanics...

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Lig - Ligands interactions.
HA - Hardware accelerated

Molecular modeling on GPU

Molecular modeling on GPU is the technique of using a graphics processing unit for molecular simulations.In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards include many arithmetic units working in parallel...

Name	View 3D	Model Build	Min	MD	MC	REM	Crt	Int	Exp	Imp	Lig	HA	Comments	License	Homepage
Abalone Abalone (molecular mechanics) Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit water or in implicit water models...	+	+	+	+	+	+	+		+	+	+	+	DNA DNA Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in... , proteins, ligands Ligand (biochemistry) In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.The binding occurs by intermolecular forces, such as ionic bonds, hydrogen...	Free	Agile Molecule
AMBER AMBER AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...		+	+	+		+	+		+	+	+		AMBER AMBER AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields... Force Field Force field (chemistry) In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...	Commercial	ambermd.org
Ascalaph Designer Ascalaph Designer Ascalaph Designer is a general purpose molecular modelling package for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling NWChem, Firefly, CP2K and MDynaMix...	+	+	+	+			+		+	+	+		AMBER AMBER AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...	GPL	biomolecular-modeling.com
CHARMM CHARMM CHARMM is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them...		+	+	+	+		+		+	+	+		CHARMM Force Field Force field (chemistry) In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...	Commercial	charmm.org
ICM ICM-Browser ICM-Browser is a free product of Molsoft, and provides access to structural biology data and protein families. It reads PDB or alignment files directly from online databases and provides a molecular graphics environment with various representations of proteins, DNA and RNA, and multiple sequence...	+	+	+		+			+		+			Global optimization Global optimization Global optimization is a branch of applied mathematics and numerical analysis that deals with the optimization of a function or a set of functions to some criteria.- General :The most common form is the minimization of one real-valued function...	Commercial	Molsoft
JUMNA		+	+					+		+				Commercial
MDynaMix MDynaMix MDynaMixis a general purpose molecular dynamics software package for simulations mixtures of molecules,interacting by AMBER/CHARMM like force fields in a periodic boundary conditions....	+	+		+			+		+		+		Common MD	GPL	Stockholm University
MOE	+	+	+	+			+		+		+		Molecular Operating Environment	Commercial	Chemical Computing Group
NAB		+											Nucleic Acid Builder	GPL	New Jersey University
NAMD NAMD NAMD is a free-of-charge molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems...	+		+	+			+		+		+	+	NAnoscale Molecular Dynamics	Free	University of Illinois

See also