# Water appearing in bilayer core during NPT

**URL:** https://gromacs.bioexcel.eu/t/water-appearing-in-bilayer-core-during-npt/12060
**Category:** User discussions
**Tags:** simulation-setup
**Created:** [May 11, 2025, 6:37am UTC](https://gromacs.bioexcel.eu/t/water-appearing-in-bilayer-core-during-npt/12060 "2025-05-11T06:37:14Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)
#### Post date: [May 11, 2025, 5:18pm UTC](https://gromacs.bioexcel.eu/t/water-appearing-in-bilayer-core-during-npt/12060/2 "2025-05-11T17:18:31Z")

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Hi,

I took a look at the snapshots from your previous [post](https://gromacs.bioexcel.eu/t/smd-pulling-of-dna-toward-asymmetric-bilayer/12038/9) 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](https://pubs.acs.org/doi/10.1021/acs.jctc.3c00085) on bicelle setup (mainly with the MARTINI force field, but adaptable to atomistic simulations).

Best regards,  
Marius

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