Targeted Protein Inclusion

[dishant7227]

Hi, I am trying to simulate a flat membrane surface with a different inclusions (proteins). So how can I localize the protein manually. After the simulation how can I get an idea about the percentage and amount of protein molecule and also size of the patch in all three directions. Thank you in advance.

[weria-pezeshkian]

You can achieve this in several ways (here are two):

1. Automated Approach via Simulation:
   Create inclusions with your desired concentration using the steps outlined in the tutorials, and generate a TSI file.
   Use the generated TSI file to start a simulation, ensuring you specify an interaction between the inclusions. Disable the vertex position update and edge flip update. This configuration allows the inclusions to cluster more quickly.
   Once the inclusions have clustered, save the final TSI file and use it to run any simulation with your desired parameters. The key point is that this TSI file contains information about the positions of the inclusions.

2. Manual Addition to the TSI File:
   Manually edit the TSI file to add inclusions. Identify the list of vertices where you want to place inclusions.
   In the TSI file, the inclusions section starts with the keyword inclusion, followed by the number of inclusions. Each inclusion entry requires five numbers:
   The index of the inclusion (starting from zero).
   The type of the inclusion.
   The ID of the vertex associated with the inclusion.
   The last two numbers, is local orientation, which you can set to 0 and 1 for the start.
   For more detailed instructions, refer to the tsi file section of the manual.
   Example of inclusion section of a tsi file.
   inclusion 3
   0 1 22 0 1
   1 1 5 0 1
   2 2 30 0 1

[dishant7227]

Thank you so much for your detailed explanation.