CoordinateSets (Node)

Generate a population of molecules from a Species
Context Generation
Name Required? Yes
Branches

Overview

The CoordinateSets node generates a population of molecules from a reference species.

Description

The CoordinateSets node generates a population of sets of coordinates of a specified species, using a particular evolution algorithm. These sets can then be used by another node, for instance the Add node in order to add “unique” molecules of different conformations to a box, rather than identical copies of the same species.

The coordinate set population is only generated once (the first time the node is run in the procedure) - subsequently the existing population will be used unless the Force option is enabled.

Options

Target

Keyword Arguments Default Description
Species name

Required

Target species to for which to generate sets of coordinates.
Source CoordinateSetSource MD Source for coordinate sets.
Force bool false Whether the generation of coordinate sets should proceed every time the node is executed. Otherwise, the population is generated on the first call only.

Source Data (if using file)

Keyword Arguments Default Description
File TrajectoryFileAndFormat File and format specifying coordinates to read in if Source == “File”.

Generation (if using MD)

Keyword Arguments Default Description
NSets int 100 Number of sets to generate.
NSteps int 2000 Number of steps between capture of sets in MD generation method.
DeltaT double 5.0e-4 Timestep to use in “MD” generation method.
Last modified October 30, 2024: feat: TR module added (#1956) (fe192b8)