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
oxDNA [6] + + + + + + + + Coarse-grained models of DNA and RNA GPL dna.physics.ox.ac.uk
YASARA + + + + + + + Interactive simulations Commercial www.YASARA.org

See also

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2

References

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