Why do pbc split bilayer?

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1

GROMACS version: 2022
GROMACS modification: No

Hi,

I completed Martini’s “Lipid Bilayer - Self Assembly” tutorial but my bilayer does not look the same as in Figure 1. For some reason, the phosphate heads are oriented towards the middle of the box, and there is a layer of water in the middle.

I apologise for these rather naive questions, but is there a way to fix this issue?

Thank you in advance for your help.

Kind regards,
Luca

2

Hi, Please post your question on the Martini forum - which can be found on their website - as it is related to Martini tutorial. If you run into any problems with GROMACS, don’t hesitate to contact our forum for support.

Additionally, to address potential periodic boundary condition (PBC) issues using GROMACS, you can find information here

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3

Hi,
In the end I figured it out.

In case anyone reading this has the same issue, what worked for me was translating the coordinates along the z-axis (with -trans) and then using ‘-pbc mol’ and ‘-ur compact’
i.e.
gmx trjconv -f dppc-md.xtc -s dppc-md.tpr -o translated.xtc -trans 0 0 3
gmx trjconv -f translated.xtc -s dppc-md.tpr -o new.xtc -pbc mol -ur compact