Remove non-adsorbed molecules
Description
This node removes molecules from a set of components if they are not adsorbed on a user-defined surface. If the molecules to be removed carry a charge, the user can also choose to remove corresponding counterions to maintain the system’s overall neutral charge. Please note that only one type of counterion can be specified. To control this process, the user must define two parameters:
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A threshold (a value between 0 and 1) to decide whether a molecule will be removed or not.
-
A timespan, which specifies the duration of the trajectory (in nanoseconds, counting from the end) that will be evaluated.
Based on the given timespan, we calculate the “average adsorption” of each molecule. This quantity is defined, for each molecule, as the number of adsorbed residues divided by the total number of residues, averaged over the analyzed trajectory. If the average adsorption of a molecule is below or equal to the threshold, the molecule will be removed; otherwise it will remain. Please note that small molecules only contain one residue, whereas large ones such as polymers typically contain several residues.
Please note that when using a threshold of 0, one single adsorption event over the entire analyzed trajectory is enough to prevent the removal of the corresponding molecule. Hence, choosing a value slightly above 0% is recommended.
Latest version
Allowed number of parents: 1
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Simulation cell containing a surface and the component to be removed.
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Molecule name |
The name of the molecules that will be removed based on their adsorption state |
selector |
component type |
empty |
N/A |
Counterion name |
The name of the molecules that will be removed based on their adsorption state |
selector |
component type |
empty |
N/A |
Threshold for removal |
Adsorption threshold below which the molecules will be removed |
float |
1>= x >= 0 |
0 |
N/A |
Timespan for average |
Timespan from the end of the simulation over which the adsorption fraction will be averaged |
float |
>0 |
5 |
ns |
Component names of the surface |
The component names of the reference group for the surface |
selector |
component types, all |
all |
N/A |
Residue names of the surface |
The residue names of the reference group for the surface |
selector |
residue types, all |
all |
N/A |