RMSD Analysis for POPC Membrane

[mostafagh98]

GROMACS version: 2024
GROMACS modification: No

Hello GROMACS Experts,

I have conducted a membrane-only (POPC) simulation and performed RMSD analysis to assess equilibration. I would like to get feedback on whether my system has equilibrated and whether extending the simulation further is necessary.

Steps I Followed :
For PBC correction, I applied the following steps in this order

• -pbc whole to make molecules whole
• -pbc nojump to remove jumps across periodic boundaries
• -center to center the membrane, selecting POPC (Group 2) as the center and System (Group 0) as output

For RMSD analysis, I used the command

gmx rms -s step7_1.tpr -f final_step7_1.xtc -tu ns -o rmsd_step7_1.xvg

I selected POPC (Group 2) for both fitting and calculation

I have some questions and would appreciate feedback from the community.

1. Is this RMSD behavior acceptable for a POPC-only membrane system? The RMSD rises initially and fluctuates near 2.5 to 3.0 nm after around 200 ns.
2. Does my RMSD suggest that the system equilibrates around 200 ns? The fluctuations seem to stabilize, but I want to confirm with experienced users.
3. Should I extend my simulation by another 100 ns for better convergence? Would additional sampling help, or does this appear stable enough?
4. For selecting the best representative structure, is RMSD clustering with the GROMOS algorithm a good approach for a membrane system? I plan to cluster based on RMSD and extract a central structure.

I appreciate any insights from the community. Thank you!

[mostafagh98]

Hi again,
I have recently extended my POPC membrane simulation from 200 ns to 300 ns, but I am still unsure whether the system has reached the plateau phase. I’ve used PBC corrections (whole, nojump) and centered the system based on POPC (Group 2).

Here are some key details:

For RMSD, I selected the POPC (Group 2) for both fitting and calculation.
I applied pbc whole to make the molecules whole, pbc nojump to remove jumps across periodic boundaries, and used -center to center the membrane (Group 2) with the system (Group 0) as the output.
I have attached two VMD images showing the first and last frames at t = 300 ns.

Despite the RMSD reaching ~3-4 nm, the system doesn’t seem to reach the plateau phase. I wonder if this is expected, or if I should extend the simulation further.
For the next step, I want to study the interaction between a peptide and the bilayer. I intend to use the best representative structure for further analysis, but I am unsure how to properly determine it. I know that clustering methods based on RMSD and the GROMOS algorithm are commonly used, but they seem less applicable for membrane systems.
I would really appreciate any insights or recommendations from the community.

Thank you for your help!