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pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions.

The current release version of pDynamo has the following capabilities:

• • Ab initio density functional theory and Hartree-Fock QC methods employing Gaussian basis sets.

  • Semi-empirical QC methods of the MNDO type, including AM1, MNDO, PDDG, PM3 and RM1.

  • Support for some standard MM force fields, including AMBER, CHARMM and OPLS-AA.

  • Hybrid QC/MM methods using any combination of the QC and MM potentials implemented in the library.

  • Coupling to third-party MM and QC programs for enhanced functionality.

  • Energy calculations.

  • Geometry optimizations.

  • Transition state searches.

  • Reaction path calculations.

  • Normal mode analyses.

  • Property calculations, such as charges and dipoles.

  • Molecular dynamics simulations.

  • Monte Carlo simulations.

  • Various geometrical restraints.

  • The ability to handle a large number of common molecular file formats.

  • Miscellaneous analysis tools.

pDynamo is written in a mixture of the scripting language, Python, and the compiled languages, Cython and C. All user interaction with the library is performed via Python scripts.