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.

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.