Water appearing in bilayer core during NPT

User discussions
1

GROMACS version: 2024.4
GROMACS modification: No

Hi everyone,

I’m working on a steered molecular dynamics (SMD) simulation studying the interaction of DNA with a lipid membrane, and I’ve encountered a puzzling issue that I hope someone here can help me with.

Initially, I set up my system using direction-periodic geometry. Since this setup shouldn’t use a dynamic box, I disabled compressibility in the z-direction. To avoid water molecules penetrating the bilayer core, I removed water within the bilayer region after solvation. I determined the bilayer core region using the gmx density tool, selecting the phosphate groups of the membrane to establish the region’s boundaries. The two peak coordinates of the phosphate group density were used as thresholds in a custom script (attached) to identify and remove any water within this region.

Despite this setup, I observed that water molecules still appeared in the bilayer core during the NPT equilibration phase, even though this didn’t occur in the NVT phase. The membrane and DNA are restrained during this process.

Suspecting that the issue might be related to the lack of compressibility in the z-direction, I switched the geometry to cylindrical, allowing me to enable compressibility in the z-direction. Unfortunately, even in this setup, water molecules continued to appear in the bilayer core during the NPT phase.

I’m genuinely confused as to why this is happening. Has anyone else experienced something similar? Is there a known solution or potential reason for water intruding into the bilayer core in such simulations?

I’d be grateful for any insights or suggestions.

Thanks in advance!

clean_water_z.txt (1.6 KB)

2

Hi,

I took a look at the snapshots from your previous post and noticed you used a lipid bicelle–like setup for your simulation. However, your bicelle appears to have large hydrophobic defects at the edges, as @obZehn already pointed out, which is a rather energetically unfavorable state.

Have you visualized your trajectory to see how water molecules penetrate the membrane? Also, why choose a bicelle setup to study DNA penetration? A standard bilayer might be easier to handle and carry fewer methodological caveats.

If you do decide to proceed with bicelles, I recommend this paper on bicelle setup (mainly with the MARTINI force field, but adaptable to atomistic simulations).

Best regards,
Marius

3

Dear @Marius,
Actually, I intended to have a full planar bilayer, but I mistakenly set the box size larger than the membrane’s XY dimensions. This caused the bilayer to behave like a nanodisk. I have now corrected it, ensuring that the box size properly matches the membrane’s XY dimensions. The edges of the bilayer now connect seamlessly to their own images in neighboring boxes, creating an infinite, stable membrane where water remains outside at all stages.