Create Layer on Surface

Description

This function takes a surface from a parent system and creates a layer of components on top of it. Similar to the create layer function, it forms a monolayer. To generate multiple layers, this function should be used recursively.

Latest version

Allowed number of parents: from 2 to N

Parent system
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

Parameter	Description	Value type	Value restrictions	Default value	Units
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	`random` `regular`	`regular`	none
Curvature of the surface	The curvature of the surface	selector	`flat` `spherical`	`flat`	none
Surface normal	Indicate the direction normal to the surface	selector	x y z	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

Number of copies of component i

Total copies of i to insert, one entry number of for each parent

int

none

Orientation

The orientation of the components to be inserted

selector

random
regular

regular

none

Curvature of the surface

The curvature of the surface

selector

flat
spherical

flat

none

Surface normal

Indicate the direction normal to the surface

selector

none

Surface radius

Indicate the radius of the spherical surface

float

>0.0

0.0

Surface center

Indicate the center of the spherical surface

float

none

[0.0, 0.0, 0.0]

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

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

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

Distance limit for energy minimization

Minimum distance between the inserted component and the existing system before the minimization

float

>0.0

0.5