How Tos
Introduction
This page complements the documentation on the pDynamo website with articles that describe in more detail the implementation and use of various important aspects of pDynamo. All code that is given is appropriate for pDynamo3 unless otherwise stated.
Array operations are ubiquitous in pDynamo scripts and in its C and Cython code. This page gives a brief introduction to the implementation of pDynamo arrays and their use.
The selection of atoms is a useful and versatile tool that is widely used in pDynamo and other modeling programs when, for example, preparing a system for simulation, or analyzing the results of a calculation. Some of the ways in which atom selections can be generated in pDynamo, together with their properties, are described here.
pDynamo reads and writes modeling and simulation files in a large number of different formats. Some of these, together with some of the principles that pDynamo uses when handling these files, are summarized in this article.
The definition of a system's force field is a crucial step in all MM and QC/MM simulation studies. pDynamo can do this using its own mechanisms, or by reading the definitions generated using third party programs.
A tutorial that shows how to set up a system for a MM molecular dynamics simulation in pDynamo starting from a PDB file.