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 lie on the same surface.

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.

Periodic boundary conditions (PBCs) can be considered when calculating the distance between atoms.

Latest version

Allowed number of parents: 1 or 2

System to be placed in layer
System to be placed in layer

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]	Angstrom
The number of components	Total to insert. We have one entry number of for each parent component components (max 2)	int	≥0	0	N/A
Orientation	The orientation of the components to be inserted	selector	random, regular	regular	N/A
Curvature of the surface	The curvature of the surface. Can be either flat or spherical.	selector	flat, spherical	flat	N/A
Surface normal	Indicate the direction normal to the surface	selector	x, y, z	z	N/A
Surface radius	Indicate the radius of the spherical surface where the components will be placed	float	>0	0.0	Angstrom
Surface center	Indicate the center of the spherical surface where the components will be placed	float	any float	[0.0, 0.0, 0.0]	Angstrom
Minimum distance between atoms	Minimum distance between the atoms of the inserted component and the existing system. We have one entry for each inserted component (maximum two entries). If only one parent is provided, this parameter controls the minimum distance between the inserted components	float	>0	2.0	Angstrom
Periodic boundary conditions	Indicates whether we have periodic boundary conditions in x,y and z	boolean	True, False	[True, True, True]	N/A
Seed for random generation	The seed used in the random generator,-1 can be selected for a random seed	int	>-1	123	N/A
Enable minimization	Indicates if a GROMACS energy minimization should be performed to increase the insertion success rate	boolean	True, False	False	N/A
Number of steps	Maximum number of steps in the energy minimization	integer	>0	5000	N/A
Convergence criterion for energy minimization	Force convergence criterion for the energy minimization	float	0 < x < 10000	100	kJ mol^-1 nm^-1
Initial step for energy minimization	The initial step size for the energy minimization	float	0 < x < 0.1	0.001	nm
Distance limit for energy minimization	If the minimization is enabled, it indicates the minimum distance between the inserted component and the existing system before the minimization	float	>0	0.5	Angstrom

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]

Angstrom

The number of components

Total to insert. We have one entry number of for each parent component components (max 2)

int

≥0

N/A

Orientation

The orientation of the components to be inserted

selector

random, regular

regular

N/A

Curvature of the surface

The curvature of the surface. Can be either flat or spherical.

selector

flat, spherical

flat

N/A

Surface normal

Indicate the direction normal to the surface

selector

x, y, z

N/A

Surface radius

Indicate the radius of the spherical surface where the components will be placed

float

0.0

Angstrom

Surface center

Indicate the center of the spherical surface where the components will be placed

float

any float

[0.0, 0.0, 0.0]

Angstrom

Minimum distance between atoms

Minimum distance between the atoms of the inserted component and the existing system. We have one entry for each inserted component (maximum two entries). If only one parent is provided, this parameter controls the minimum distance between the inserted components

float

2.0

Angstrom

Periodic boundary conditions

Indicates whether we have periodic boundary conditions in x,y and z

boolean

True, False

[True, True, True]

N/A

Seed for random generation

The seed used in the random generator,-1 can be selected for a random seed

int

>-1

123

N/A

Enable minimization

Indicates if a GROMACS energy minimization should be performed to increase the insertion success rate

boolean

True, False

False

N/A

Number of steps

Maximum number of steps in the energy minimization

integer

5000

N/A

Convergence criterion for energy minimization

Force convergence criterion for the energy minimization

float

0 < x < 10000

100

kJ mol^-1 nm^-1

Initial step for energy minimization

The initial step size for the energy minimization

float

0 < x < 0.1

0.001

Distance limit for energy minimization

If the minimization is enabled, it indicates the minimum distance between the inserted component and the existing system before the minimization

float

0.5

Angstrom