Create Formulation Based on Concentrations
Description
This function can be used to create formulations targeting a specific concentrations for their components and a given density overall. 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. Note that the sum of all the concentrations must yield 100%. 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, which has the following options:
-
according to molecular weight of parents (heaviest first): heavier components tend to be more voluminous. Therefore, inserting first the heavier systems usually facilitates the insertion of all the molecules. -
according to hierarchy of parents: the insertion order will follow the hierarchy list that the user defines. -
random: no particular order is followed.
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, 0.0] |
Å |
Target concentration for component i |
Defines the concentration of parent i in the final formulation |
int |
≥0 |
0 |
% w/w |
Insertion ordering |
Criteria to determine the ordering of insertion |
selector |
|
|
none |
Density of the formulation |
Target density of the formulation. |
float |
>0.0 |
0.0 |
g/cm3 |
Orientation |
The orientation of the components to be inserted |
selector |
|
|
none |
Position |
Method to determine the insertion of the component |
selector |
|
|
none |
Minimum distance of parent i |
Minimum distance of insertion of parent i. |
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 |
Enable axis insertion restriction |
It limitates the regions of the cell where the selected molecules can be inserted |
boolean |
True, False |
False |
None |
Component name for axis restriction |
Component name of the molecule whose insertion is restricted |
selector |
component name |
empty |
none |
Minimum and maximum distances to cell sides on the i axis |
Distances to be kept with the limits of the cell in the i axis |
floating-point number |
≥ 0 |
[0, 0] |
Å |