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!