Getting Started

This tutorial provides a gentle introduction to pDynamo by using some of the simpler examples in the book/examples subdirectory of the pDynamo distribution. The calculations that are performed here concern small molecular systems in vacuum only. Simulations of solvated molecules and other condensed-phase systems are treated in other tutorials. Readers wanting a more in-depth discussion of the example programs and the simulation algorithms that they employ should refer to the second edition of the Dynamo book.

The logical order in which to follow the items in this tutorial is given in the list below.

Python

Basic Python programming.

Molecular Systems

Defining and manipulating molecular systems for simulation.

Quantum Chemical Calculations

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

Molecular Mechanical Methods

Setting up a molecular mechanics calculation.

Hybrid Potentials

Combining QC and MM methods to study a molecular system.

Geometry Optimization

Finding molecular geometries of low potential energy.

Reaction Paths

Optimization techniques for investigating chemical reactions and conformational transitions.

Normal Mode Analysis

Dynamics of molecular systems within the harmonic approximation.

Molecular Dynamics

Going beyond the harmonic approximation.