Create Layer
Description
This function creates a layer of components, specifically a monolayer, meaning the geometric center of each added copy of the parent systems will have all the same coordinate along the direction of the layer normal. The layer can either be spherical or flat, with the points evenly distributed across the surface. For spherical surfaces, the golden spiral method is used, while for flat surfaces, the space-filling curve is applied. The density of points is determined by the combination of the cell size and the number of systems to insert. However, to prevent overlap due to random orientations of molecules, we ensure that no molecules are closer than the specified minimum distance input. If only one parent is provided, this parameter controls the minimum distance between the inserted components Periodic boundary conditions (PBCs) can be considered when calculating the distance between atoms to avoid close contacts between molecules.
Latest version
Allowed number of parents: from 1 to N
-
Any system that will form a monolayer. A number of components will be associated to each one of them.
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Cell dimensions |
The three cell lengths (x, y, z) |
float |
>0.0 |
[0.0, 0.0, 0.0] |
Å |
Number of copies of component i |
Total copies of i to insert, one entry number of for each parent |
int |
>0 |
0 |
none |
Orientation |
The orientation of the components to be inserted |
selector |
|
|
none |
Curvature of the surface |
The curvature of the surface |
selector |
|
|
none |
Surface normal |
Indicate the direction normal to the surface |
selector |
|
z |
none |
Surface radius |
Indicate the radius of the spherical surface |
float |
>0.0 |
0.0 |
Å |
Surface center |
Indicate the center of the spherical surface |
float |
none |
[0.0, 0.0, 0.0] |
Å |
Minimum distance of parent i |
Minimum distance the inserted component and the existing system, one entry for each inserted component. |
float |
>0.0 |
2.0 |
Å |
Seed for random generation |
The seed used in the random generator, -1 can be selected for a random seed |
int |
≥-1 |
123 |
none |
Periodic boundary conditions |
Indicates whether we have periodic boundary conditions in x, y and z |
boolean |
True, False |
[True, True,True] |
none |
Enable minimization |
Indicates if a GROMACS energy minimization should be performed to increase the insertion success rate |
boolean |
True, False |
False |
none |
Number of steps |
Maximum number of steps in the energy minimization |
integer |
>0 |
5000 |
none |
Convergence criterion for energy minimization |
Force convergence criterion |
float |
0.0 < x < 10000.0 |
100.0 |
kJ mol-1 nm-1 |
Initial step for energy minimization |
The initial step size |
float |
0.0 < x < 0.1 |
0.001 |
nm |
Distance limit for energy minimization |
Minimum distance between the inserted component and the existing system before the minimization |
float |
>0.0 |
0.5 |
Å |