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

Parameter	Description	Value type	Value restrictions	Default value	Units
Concentration	Target concentration of the inserted component(s)	float	≥0.0	0.0	% w/w
Solvent name	Name of the solvent	selector	component names	empty	none
Insertion ordering	Criteria to determine the ordering of insertion	selector	`according to hierarchy of parents` `random` `according to molecular weight of parents (heaviest first)`	`according to molecular weight of parents (heaviest first)`	none
Orientation	The orientation of the components to be inserted	selector	`random` `regular`	`random`	none
Position	Method to determine the insertion of the component	selector	`random` `spacefilling`	`random`	none
Minimum distance of inserted component	Minimum distance between the inserted component and the closest atom of the system	float	>0.0	2.0	Å
Periodic boundary conditions	Indicates whether we have periodic boundary conditions in x, y and z	boolean	True, False	[True, True,True]	none
Seed for random generation	The seed used in the random generator, -1 can be selected for a random seed	int	≥-1	123	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

Concentration

Target concentration of the inserted component(s)

float

≥0.0

0.0

% w/w

Solvent name

Name of the solvent

selector

component names

empty

none

Insertion ordering

Criteria to determine the ordering of insertion

selector

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

according to molecular weight of parents (heaviest first)

none

Orientation

The orientation of the components to be inserted

selector

random
regular

random

none

Position

Method to determine the insertion of the component

selector

random
spacefilling

random

none

Minimum distance of inserted component

Minimum distance between the inserted component and the closest atom of the system

float

>0.0

2.0

Periodic boundary conditions

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

boolean

True, False

[True, True,True]

none

Seed for random generation

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

int

≥-1

123

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