Surface Deposit Characterization

Description

This node provides a series of analyses assessing the adsorption of a polymer (or other kind of molecules) on a surface, and it is conceived as a more thorough and complete version of the Adsorption on Surface analysis node. There are two main improved points in this node:

It can handle the existence of adsorbed multi-layers of a single molecule type on top of a surface. The user can control how many layers shall be considered for the analysis through the maximum connectivity level parameter. This contrasts with the Adsorption on Surface analysis node, which only considered for the analysis those residues of the polymer (or molecules, respectively) that were directly adsorbed on the surface.
It facilitates the automatic execution of frequently demanded analyses of adsorption nodes, as the assessment of the percentage of adsorbed molecules or the percentage of covered surface.

Latest version

Allowed number of parents: 1

Parameter Description Value type Value restrictions Default value Units

Parameter	Description	Value type	Value restrictions	Default value	Units
Names of molecules	Indicate the name of the molecules whose adsorption will be analyzed	selector component	component types, “all”	N/A	N/A
Surface zone 1: name	Name to assign to the first selected zone	str	N/A	N/A	N/A
Surface zone 1: component names	The component names of the reference group for the first surface zone	selector_component	component types, “all”	N/A	N/A
Surface zone 1: residue names	The residue names of the reference group for the first surface zone	selector_residue	residue types, “all”	`all`	N/A
Surface zone 1: atom type	The atom types of the reference group for the first surface zone	selector_atom_type	atom_types, “all”	`all`	N/A
Surface zone 1: atom name	The atom names of the reference group for the first surface zone	selector_atom	atom_names, “all”	N/A	N/A
Surface zone 2: name	Name to assign to the second selected zone	str	N/A	N/A	N/A
Surface zone 2: component names	The component names of the reference group for the second surface zone	selector_component	component types, “all”	N/A	N/A
Surface zone 2: residue names	The residue names of the reference group for the second surface zone	selector_residue	residue types, “all”	`all`	N/A
Surface zone 2: atom type	The atom types of the reference group for the second surface zone	selector_atom_type	atom_types, “all”	`all`	N/A
Surface zone 2: atom name	The atom names of the reference group for the second surface zone	selector_atom	atom_names, “all”	N/A	N/A
Direction perpendicular to surface	The direction perpendicular to the surface	selector	“x”, “y”, “z”	“z”	N/A
Use PBC in direction perpendicular to surface	Whether to use periodic boundary conditions in a perpendicular direction to the surface	bool	True, False	True	N/A
Contact distance	Distance below which molecule and surface are considered in contact	float	>0	5	angstrom
Consider H	Indicate whether to consider hydrogen atoms in the analysis	bool	True, False	False	N/A
Time considered for average	Indicate whether to average the properties over the whole simulation or just over a fraction of it	selector	entire simulation or time value	entire simulation	N/A
Time value	Time over which the properties are computed if 'time value' is selected in the previous parameter, counted backwards from the end of the trajectory	float	>0	1000	ps
Maximum connectivity level	Indicates up to which level the average is performed. The first level is identified by the molecules that are adsorbed on the surface, while the following levels are identified by the molecules that are stacked on top of the molecules belonging to the previous level.	integer	[0,1000]	0	N/A
Minimum percentage of adsorbed residues	Indicates the minimum percentage of residues of a molecule that must be in contact with the surface to consider that the molecule is adsorbed	float	[0,1000]	0	N/A
Minimum percentage of connected residues	Indicates the minimum percentage of residues of a molecule that must be in contact with another molecule to consider that the molecule is connected	float	[0,1000]	0	N/A
Calculate adsorption percentage	Indicates whether to calculate the percentage of adsorbed molecules considering both surface zones	boolean	True, False	True	N/A
Calculate coverage of the surface	Indicates whether to calculate the percentage of the total surface area that is covered with adsorbed molecules	boolean	True, False	True	N/A
Calculate thickness of the deposit	Indicates whether to calculate the thickness of the deposit	boolean	True, False	True	N/A
Calculate density	Indicates whether to calculate the density of the deposit	boolean	True, False	True	N/A
Calculate the contact matrix molecule-surface	Indicates whether to calculate the contact matrix between the molecules and the surface	boolean	True, False	True	N/A
Calculate the contact matrix molecule-molecule	Indicates whether to calculate the self-contact matrix between the molecules	boolean	True, False	True	N/A

Names of molecules

Indicate the name of the molecules whose adsorption will be analyzed

selector component

component types, “all”

N/A

Surface zone 1: name

Name to assign to the first selected zone

str

N/A

Surface zone 1: component names

The component names of the reference group for the first surface zone

selector_component

component types, “all”

N/A

Surface zone 1: residue names

The residue names of the reference group for the first surface zone

selector_residue

residue types, “all”

all

N/A

Surface zone 1: atom type

The atom types of the reference group for the first surface zone

selector_atom_type

atom_types, “all”

all

N/A

Surface zone 1: atom name

The atom names of the reference group for the first surface zone

selector_atom

atom_names, “all”

N/A

Surface zone 2: name

Name to assign to the second selected zone

str

N/A

Surface zone 2: component names

The component names of the reference group for the second surface zone

selector_component

component types, “all”

N/A

Surface zone 2: residue names

The residue names of the reference group for the second surface zone

selector_residue

residue types, “all”

all

N/A

Surface zone 2: atom type

The atom types of the reference group for the second surface zone

selector_atom_type

atom_types, “all”

all

N/A

Surface zone 2: atom name

The atom names of the reference group for the second surface zone

selector_atom

atom_names, “all”

N/A

Direction perpendicular to surface

The direction perpendicular to the surface

selector

“x”, “y”, “z”

“z”

N/A

Use PBC in direction perpendicular to surface

Whether to use periodic boundary conditions in a perpendicular direction to the surface

bool

True, False

True

N/A

Contact distance

Distance below which molecule and surface are considered in contact

float

angstrom

Consider H

Indicate whether to consider hydrogen atoms in the analysis

bool

True, False

False

N/A

Time considered for average

Indicate whether to average the properties over the whole simulation or just over a fraction of it

selector

entire simulation or time value

entire simulation

N/A

Time value

Time over which the properties are computed if 'time value' is selected in the previous parameter, counted backwards from the end of the trajectory

float

1000

Maximum connectivity level

Indicates up to which level the average is performed. The first level is identified by the molecules that are adsorbed on the surface, while the following levels are identified by the molecules that are stacked on top of the molecules belonging to the previous level.

integer

[0,1000]

N/A

Minimum percentage of adsorbed residues

Indicates the minimum percentage of residues of a molecule that must be in contact with the surface to consider that the molecule is adsorbed

float

[0,1000]

N/A

Minimum percentage of connected residues

Indicates the minimum percentage of residues of a molecule that must be in contact with another molecule to consider that the molecule is connected

float

[0,1000]

N/A

Calculate adsorption percentage

Indicates whether to calculate the percentage of adsorbed molecules considering both surface zones

boolean

True, False

True

N/A

Calculate coverage of the surface

Indicates whether to calculate the percentage of the total surface area that is covered with adsorbed molecules

boolean

True, False

True

N/A

Calculate thickness of the deposit

Indicates whether to calculate the thickness of the deposit

boolean

True, False

True

N/A

Calculate density

Indicates whether to calculate the density of the deposit

boolean

True, False

True

N/A

Calculate the contact matrix molecule-surface

Indicates whether to calculate the contact matrix between the molecules and the surface

boolean

True, False

True

N/A

Calculate the contact matrix molecule-molecule

Indicates whether to calculate the self-contact matrix between the molecules

boolean

True, False

True

N/A