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. pDynamo is written in a mixture of Python and C and complements the existing version of Dynamo, now denoted fDynamo, that is written in Fortrans 90 and 95.

The current release version of pDynamo has the following capabilities:

  • A density functional theory QC method 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 QC programs.
  • 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 "soft" geometrical constraints.
  • The ability to handle various common molecular file formats.
  • Miscellaneous analysis tools.