This tutorial provides a gentle introduction to pDynamo by using some of the simpler examples in the
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.