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
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Cell full of solvent
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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 |
Minimal distance between atoms |
Minimal distance between two 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 |