Assistance Needed with Pulling a Protein Aggregate Through a Protein Pore

Hello everyone,

I’m working on a molecular dynamics simulation in GROMACS where my objective is to pull an entire protein aggregate through the central pore of another protein. In my system, represented in a PDB/GRO file, I have two proteins. To accomplish this task, I’ve created four index groups: ‘aggregated_protein’, ‘c_terminal’ (of the aggregated protein), ‘pore_protein’ (the protein with the central pore), and ‘loop_location’ (a location at the end of the pore).

My goal is to pull the whole aggregated protein through the pore of the second protein by targeting the C-terminal of the aggregated protein. However, I’m facing challenges in achieving this. Below are the scenarios I’ve tried with their respective GROMACS pull codes and the issues I encountered:

Scenario One:
This setup only pulls the C-terminal, not the entire aggregated protein.
; Pull code
pull = yes
pull_ngroups = 2 ; Two groups involved
pull_group1_name = pore_protein ; protein containing the central pore as reference group
pull_group2_name = c_terminal ; Atom to be pulled, C-terminal of the aggregated protein

pull_ncoords = 1 ; One coordinate for pulling

; Define pull coordinates
pull-coord1-type = constant-force ; constant-force
pull-coord1-groups = 1 2 ; 1 for absolute reference, 2 for the atom
pull-coord1-geometry = direction ; Pulling in a specified direction
pull-coord1-dim = Y N N ; Pulling only in X direction
pull-coord1-start = yes ; Start from the initial configuration
pull-coord1-vec = -1 0 0 ; Direction vector for pulling (along X-axis)
pull-coord1-k = 1000 ; Force constant
Scenario Two : In this case, the entire aggregated protein is being pulled, but not through the pore.
; Pull code
[Similar to Scenario One, with pull_group2_name set to ‘aggregated_protein’]
Scenario Three : Similar to Scenario One, this setup also only pulls the C-terminal, not the entire aggregated protein.
; Pull code
[Similar to Scenario One, with pull_group1_name set to ‘loop_location’]

In each scenario, I am not achieving the desired result of pulling the entire aggregated protein through the central pore of the other protein. I would greatly appreciate any insights or suggestions on how to modify my pull code or simulation setup to accomplish this task.

Thank you in advance for your help!

You need to place the molecule that you need to pull carefully at the pore region. You can place them in the middle of the ‘channel’ and pull it through the ‘periodic’. Later remove the parts that you dont need from the trajectory.
It is challanding to pull through a ‘channel’ especailly if you your pulling a ‘protein or peptide’-