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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,

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 Crt Int Exp Imp Lig HA Comments License Homepage
Abalone ++++ + +++ DNA, proteins, ligands Free Agile Molecule
AMBER | +++ + +++ AMBER Force Field Commercial ambermd.org
CHARMM +++++ +++ CHARMM Force Field Commercial charmm.org
ICM| + + + + + + Global optimization Commercial Molsoft
JUMNA | ++ + + Commercial
MDynaMix [1] ++ + + + + Common MD GPL Stockholm University
MOE ++++ + + + Molecular Operating Environment Commercial Chemical Computing Group
NAB | + Nucleic Acid Builder GPL New Jersey University
NAMD + ++ + + ++ NAnoscale Molecular Dynamics Free University of Illinois

See alsoEdit

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