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.