CoordinateSets (Node)
Generate a population of molecules from a Species
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. |