Contributions
This page contains contributions from users illustrating how to perform modeling and simulation tasks with pDynamo that are not treated directly in the official distribution. Each contribution contains the name of the contributor and the pDynamo version for which it was written. Although many of these contributions will have been designed for the older Python 2 versions of pDynamo, they should be useful as templates for users wishing to adapt them to pDynamo3.
Coupling integrals are one of the ingredients needed for the evaluation of electron and hole transfer rates in Marcus theory and its generalizations. This page provides an example of the calculation of the coupling integrals from the molecular orbitals and the orbital energies of two neighboring molecules.
pDynamo has several features allowing the simulation of organic crystals. This tutorial illustrates some of these features using paracetamol as an example.
Sometimes it is necessary to define a new atom type and to specify the force field parameters associated with it. This simple tutorial shows how to extend the OPLS-AA force field for proteins so as to deal with paracetamol.
This tutorial explains how to perform QC/MM calculations with pDynamo using Orca as the external QC program. This gives access to more QC methods than the ones available in pDynamo, and will also be more efficient, especially for large systems run in parallel on several processors.
Two parameter sets for semiempirical QC methods are described that have been developed to give better energetic and structural results for halide substitutions and phosphate reactions.
An intuitive and interactive graphical environment designed to assist pDynamo3 users with various tasks. EasyHybrid is a useful tool that simplifies the process of working with pDynamo3Â package.