GROMACS version:
GROMACS modification: Yes/No
Here post your question
Dear users,
I need to calculate the mean square displacement (MSD) of polymer units from the oil-water interface using GROMACS. Since the system contains a double interface, I am interested in analyzing the diffusion of the polymer from only one interface, located at z = 2.5 nm, into the aqueous phase. Specifically, I want to calculate the diffusion from z = 2.5 nm to z = 7.5 nm. How can I define this distance range in the gmx msd command?
This is a non-trivial problem. Diffusion is about displacement and you want to calculate something localized.
You can select the group of molecules to analyze based on position. I assume this if based on the initial frame. Then you need to take into account that this selection will diffuse.
Thank you, sir, for your reply. I have calculated the diffusion coefficients using the command: gmx msd -f md.xtc -s md.tpr -o msd-msd.xvg.
I examined two oil-water systems with double interfaces, each containing different types of polymers. In system A, which includes polymer A, the polymer is confined to the interface, while in system B, which contains polymer B, the polymer is more diffused into the water phase.
The diffusion coefficient D of system A (with polymer A) is 0.3508 (+/- 0.0926) × 10⁻⁵ cm²/s, which is higher than that of system B (with polymer B), which has a diffusion coefficient D of 0.1899 (+/- 0.2129) × 10⁻⁵ cm²/s.
However, these values are opposite to what I initially expected, and I am now unsure whether I am on the right path with my calculations. Is there any modification should I do with the command?
Could you kindly help me address this issue? I am attaching the image of the system after MD run
