Gromacs  2016.4
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Dynamic selections

The Parsing and Evaluation of Analysis Selections (selection) module provides a mechanism that allows selections specified as text, and the engine evaluates them to atoms, or more generally to a set of positions, for one or more sets of coordinates. The selected atoms can depend on the trajectory frame. This allows writing general-purpose analysis tools that only operate on positions, and get a lot of flexibility for free from the selection engine. For example, such tools can readily operate on centers of mass of groups in addition to individual atoms as long as they do not require access to atomic properties.

For people familiar with VMD, the selection syntax is quite familiar, but there are some differences. Not all the keywords supported by VMD are there, and there are some extensions related to the support to evaluate to center-of-mass positions in addition to individual atoms. For old-time GROMACS users, tools that support selections do not generally need make_ndx.

Structural overview

Central concepts useful for understanding the selection engine are explained below. A graph represents the relations between the different parts, and a textual description of the user-visible components and other concepts follows. The graph also includes an overview of how the selection engine integrates into the Framework for trajectory analysis. When using selections from the analysis framework, the parts in gray are managed by the framework. When using selections outside the framework, it is either possible to use only the core components (shown in the graph as a box), or to also use the selection option mechanisms. In both cases, the caller is responsible of managing all the objects owned by the framework in the graph.

Core selection engine

The core of the selection engine is the selection collection object. The graph below shows how it handles selections. The operations that the collection object supports and their sequence is shown in the boxes in the middle. Inputs are shown at top, and outputs at the bottom.