Modify Formulation Based on Concentrations

Description

This node receives a cell full of solvent and at least one additional component node to substitute solvent molecules by the new component(s). This system operation function can be useful to simulate a dynamic environment in which the concentration of some component must vary.

Latest version

Allowed number of parents: 2 or more

Cell full of solvent
Component to insert

Parameter	Description	Value type	Value restrictions	Default value	Units
Concentration	Target concentration of the inserted component(s)	float	>=0	0	% w/w
Solvent name	Name of the solvent	selector	component names	empty	N/A
Insertion ordering	The ordering of insertion of the copies of the molecules	selector	according to hierarchy of parents, random, according to molecular weight of parents (heaviest first), evenly distributed	according to molecular weight of parents (heaviest first)	N/A
Orientation	The orientation of the components to be inserted	selector	random, regular	random	N/A
Position	The position within the cell where the components shall be inserted	selector	random, spacefilling	random	N/A
Minimum distance between atoms of the original system and the inserted components	Minimum distance between the atoms of the inserted component and the existing system. This minimum distance does not apply to the solvent molecules that will be removed due to the overlapping with an inserted component.	float	>0	2.0	Angstrom
Minimum distance between inserted components	Minimum distance between the atoms of 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

Concentration

Target concentration of the inserted component(s)

float

>=0

% w/w

Solvent name

Name of the solvent

selector

component names

empty

N/A

Insertion ordering

The ordering of insertion of the copies of the molecules

selector

according to hierarchy of parents, random, according to molecular weight of parents (heaviest first), evenly distributed

according to molecular weight of parents (heaviest first)

N/A

Orientation

The orientation of the components to be inserted

selector

random, regular

random

N/A

Position

The position within the cell where the components shall be inserted

selector

random, spacefilling

random

N/A

Minimum distance between atoms of the original system and the inserted components

Minimum distance between the atoms of the inserted component and the existing system. This minimum distance does not apply to the solvent molecules that will be removed due to the overlapping with an inserted component.

float

2.0

Angstrom

Minimum distance between inserted components

Minimum distance between the atoms of 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