Orient system
Description
This function orients the system along a specified axis and direction along that axis.
The function aligns the system’s principal axis along the x, y, or z axis. The orientation (positive or negative direction) is determined by comparing the system’s geometric center with the position of a selected atom. The user can choose whether the selected atom should be positioned below or above the geometric center.
IMPORTANT NOTE: The orientation is applied to the entire system, using the principal axis of the whole system. It is recommended to orient individual molecules before adding them to more complex simulation cells.
Latest version
Allowed number of parents: 1
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Axis to orient the system along |
Indicate the axis along which the principal axis of the system will be aligned |
selector |
x, y, z |
Z |
N/A |
Position of selected atom respect to the system’s geometric center |
This choice will determine the orientation of the system |
selector |
up, down |
up |
N/A |
Component name of reference atom |
Indicate the component name of the reference atom |
selector_component |
component types, “all” |
N/A |
N/A |
Residue name of reference atom |
Indicate the residue name of the reference atom |
selector_residue |
residue types, “all” |
|
N/A |
Atom type of reference atom |
Indicate the component name of the reference atom |
selector_atom_type |
atom_types, “all” |
|
N/A |
Atom name of reference atom |
Indicate the atom name of the reference atom |
selector_atom |
atom_names, “all” |
N/A |
N/A |