Create Formulation Based on Concentrations

Description

This function can be used to create formulations targeting a specific density and that contain several molecules at a given concentration. This function can have an unlimited number of parents.
A concentration (in weight percentage, % w/w) must be associated with every parent through the corresponding input.
Starting from the concentrations, the definition of a simulation cell and a target density, the number of copies of parent molecules to insert in the system is calculated.
The order of insertion in the system is controlled by the input Insertion ordering. Except for specific cases, it is recommended to insert the heaviest molecules first.
The other inputs, which control some features of the insertion procedure, are the same as those of the create and fill cell function.

Latest version

Allowed number of parents: from 2 to N

Any system that wants to be inserted. A concentration will be associated to each one of them

Parameter	Description	Value type	Value restrictions	Default value	Units
Cell dimensions	The three cell lengths (x,y,z)	float	>0	[0.0, 0.0, 0.0]	Angstrom
Target concentration for component i	One for every parent, defines the concentration of that parent in the final formulation.	int	>0	0	% w/w
Insertion ordering	The ordering of insertion of the copies of the parent molecules	selector	according to hierarchy of parents, random, according to molecular weight of parents (heaviest first)	according to molecular weight of parents (heaviest first)	N/A
Density of the formulation	The target density of the formulation. Together with the concentrations indicated for each component and the cell volume, determines the actual number of molecules that will be inserted	float	>0	0	g/cm3
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.	float	>0	2.0	Angstrom
Minimum distance of parent i	Minimum distance of insertion of parent i.	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

Cell dimensions

The three cell lengths (x,y,z)

float

[0.0, 0.0, 0.0]

Angstrom

Target concentration for component i

One for every parent, defines the concentration of that parent in the final formulation.

int

% w/w

Insertion ordering

The ordering of insertion of the copies of the parent molecules

selector

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

according to molecular weight of parents (heaviest first)

N/A

Density of the formulation

The target density of the formulation. Together with the concentrations indicated for each component and the cell volume, determines the actual number of molecules that will be inserted

float

g/cm3

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.

float

2.0

Angstrom

Minimum distance of parent i

Minimum distance of insertion of parent i.

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