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.