This extension provides the possibility to place molecules on surfaces.

Documentation

1. Select the system based on which the surface should be created. Click the corresponding Set button.
2. Select the structure that you want to put on top of the surface. Click the corresponding Set button. Please note that the way new structures will be added to the document’s data graph depends on the level of selection of the structure: if you select a structural model then new structures will be added right to the document as copies of the original structural model. If you select a molecule or a structural group/residue then they will be added directly to the system’s structural model.
3. Set the number of structures that you want to place on the surface and the distance between the surface and the selected structure’s atom.
4. [Optional] Select the structure’s atom which should be the closest to the surface. Click the corresponding Set button. If not set then it will be auto-detected as the structure's atom closest to the surface.
5. [Optional] Change how the added structures should be oriented on the surface.
6. Once you set up the system, click Run. If it wasn’t possible to place the required number of structures on the surface on the first try, then it will try to smooth the surface and try placing the structures again – this might be repeated up to 10 times and, in the end, the placement with the maximum number of structures on the surface will be selected.

The grafting density is computed and displayed in the results.

Orientation of structures

By default, the newly added structures are oriented based on the sum of the normal to the surface and the vector from the center, which should be the best for sphere- or ellipsoid-like surfaces. You can modify the orientation option in the interface.

References

Miroslava Nedyalkova, Giovanni Russo, Philip Loche, and Marco Lattuada. Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics. J. Chem. Inf. Model. 2023, 63, 23, 7453–7463. https://doi.org/10.1021/acs.jcim.3c01547

This extension was developed thanks to grant КП-06-Н59/10: Ionic Liquids & Molecular dynamics & Machine Learning - a road for of opening new drug carriers.