Set Charge
Description
This function sets the charge of a system. It requires the main system as the first parent and one or two
charged system as the second/third parent. If two charged systems are selected as parents,
they must carry a charge of opposite sign. Otherwise, the function is not able to decide
which charged system to use and it will raise an error.
The function automatically calculates how many copies of the second/third system need to be inserted
into the main system to reach the specified target_charge.
Once the required number of copies is determined, a fill_cell operation is performed, with random
position and random orientation of the molecules in the cell (see here for
more details).
Latest version
Allowed number of parents: 2 or 3
-
Main System
-
Charged system to be inserted in the Main System
-
Second (optional) charged system, must have a charge of opposite sign compared to the first charged system
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Target charge |
The charge of the final system in units of electrons. |
int |
N/A |
0 |
e |
Minimum distance between atoms |
Minimum distance between the atoms of the inserted component and the existing system. We have one entry for each inserted component (maximum two entries) |
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 |