This section contains user-contributed "howtows", illustrating the use of pDynamo for specific modelling tasks.
Please have a look also at the Getting Started, the Tutorials, the Documentation, the Library Reference and the Useful Links on the official pDynamo site.
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.
pDynamo has several features allowing the simulation of organic crystal structures. This tutorial illustrates some of these features, using again paracetamol as an example.
This page provides an example of the calculation of the coupling integrals (one ingredient for the evaluation of electron/hole transfer rates, according to the Marcus theory and its generalizations) from the molecular orbitals and the orbital energies of two neighbouring molecules.
This shows how to follow the Intrinsic Reaction Coordinate (IRC) for a reaction and produce a file which can be visualized with VMD.
QC/MM calculations with Orca and pDynamo
This tutorial explains how to perform QC/MM calculations with pDynamo using Orca as the external QC program. This allow to use more basis sets, functionals and QC methods than the ones available in pDynamo. It will also be more efficient, especially for large systems run in several processors in parallel.