The pDynamo Program

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.