NAMD

NAMD (NAnoscale Molecular Dynamics)¹is 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 (millions of atoms). It has been developed by the joint collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana-Champaign.

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It was introduced in 1995 by Nelson et al. as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling to thousands of processors. The latest version (as of January 2007) is 2.6, one new feature of which is support for the OPLS force field.

See also

• CHARMM
• Grace (plotting tool)
• VMD
• Charm++

References

¹ Flexibility and Interoperability in a Parallel Molecular Dynamics Code, postscript file

² NAMD A Parallel Object-Oriented Molecular Dynamics Program, pdf file