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NAMD is a parallel molecular dynamics code for large biomolecular systems. NAMD is free with source code.

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AMMP Home Page Welcome to AMMP AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and ...

EGO - A Program for Efficient Parallel Molecular Dynamics ...