This section gives a gentle introduction to pDynamo3 usage by presenting examples that are described in detail in the second edition of the Dynamo book. The scripts for these examples are included in the pDynamo3 distribution, together with an extensive series of other examples, tests and tutorials. Many of these, together with other contributions about pDynamo usage, are discussed in the wiki.

The calculations that are performed in this section concern small molecular systems in vacuum only. Scripts for the simulation of solvated molecules and other condensed-phase systems may be found in the distributions and the wiki.

The logical order in which to follow the items in this section is listed below. The scripts that are discussed may be found in the examples/book subdirectory of the pDynamo3 distribution. Note too that the descriptions use python3 to invoke the Python3 interpreter, although the actual command may differ depending on the system that the examples are being run on.

Basic Python programming.

Defining and manipulating molecular systems for simulation.

Employing simple quantum chemical (QC) techniques to determine potential energies and other molecular properties.

Setting up a molecular mechanics (MM) calculation.

Combining QC and MM methods to study a molecular system.

Finding molecular geometries of low potential energy.

Optimization techniques for investigating chemical reactions and conformational transitions.

Dynamics of molecular systems within the harmonic approximation.

Going beyond the harmonic approximation.