Free molecules

Description

This function yields the percentage of a specific group of molecules that is not adsorbed on a surface nor aggregated by their own or with third species. The user must define the molecule and the surface, and a third chemical species called 'inhibitor' can also be specified. Inhibitors are molecules that form aggregates along with the specified molecule, and thus they are 'inhibiting' the contact between these molecules. The molecules that form an aggregate with the inhibitors will not be accounted as free molecules. Also, a maximum number of nearby molecules that are considered free can be defined.

Latest version

Allowed number of parents: 1

Parameter	Description	Value type	Value restrictions	Default value	Units
Component names to be considered for the analysis	Indicate the name of the components to be considered for the analysis	selector	component types, all	all	N/A
Inhibitor component names	Indicate the name of inhibitor that could prevent the aggregation of the molecule to be analyzed	selector	component types, empty	empty	N/A
Aggregation cutoff	Indicate the cutoff for the aggregation analysis	float	>0	3.5	Angstrom
Maximum number of nearby molecules to be considered free	Maximum number of molecules below the aggregation cutoff that are considered to be free. For most cases, this value can be set to 1	integer	>0	1	number of components
Component names of the surface	The component names of the surface	selector	component types, all	all	N/A
Residue names of the surface	The residue names of the surface	selector	residue types, all	all	N/A
Atom types of the surface	The atom types of the surface	selector	atom types, all	all	N/A
Atom names of the surface	The atom names of the surface	selector	atom names, all	all	N/A
Direction perpendicular to the surface	The direction perpendicular to the surface	selector	x,y,z	z	N/A
Apply PBC perpendicular to the surface	Indicate whether to use periodic boundary conditions in the perpendicular direction to the surface	boolean	True, False	True	N/A
Contact distance	Distance below which molecule and surface are considered in contact	float	>0	5	Angstrom
Consider hydrogen atoms	Indicate whether to consider hydrogen atoms in the analysis	boolean	True, False	False	N/A
Stride	Indicate the stride for the analysis	float	>=0	10.0	ps

Parameter

Description

Value type

Value restrictions

Default value

Units

Component names to be considered for the analysis

Indicate the name of the components to be considered for the analysis

selector

component types, all

all

N/A

Inhibitor component names

Indicate the name of inhibitor that could prevent the aggregation of the molecule to be analyzed

selector

component types, empty

empty

N/A

Aggregation cutoff

Indicate the cutoff for the aggregation analysis

float

3.5

Angstrom

Maximum number of nearby molecules to be considered free

Maximum number of molecules below the aggregation cutoff that are considered to be free. For most cases, this value can be set to 1

integer

number of components

Component names of the surface

The component names of the surface

selector

component types, all

all

N/A

Residue names of the surface

The residue names of the surface

selector

residue types, all

all

N/A

Atom types of the surface

The atom types of the surface

selector

atom types, all

all

N/A

Atom names of the surface

The atom names of the surface

selector

atom names, all

all

N/A

Direction perpendicular to the surface

The direction perpendicular to the surface

selector

x,y,z

N/A

Apply PBC perpendicular to the surface

Indicate whether to use periodic boundary conditions in the perpendicular direction to the surface

boolean

True, False

True

N/A

Contact distance

Distance below which molecule and surface are considered in contact

float

Angstrom

Consider hydrogen atoms

Indicate whether to consider hydrogen atoms in the analysis

boolean

True, False

False

N/A

Stride

Indicate the stride for the analysis

float

>=0

10.0