# My production file - periodic boundary

**URL:** <https://gromacs.bioexcel.eu/t/my-production-file-periodic-boundary/11466>\
**Category:** User discussions\
**Created:** [February 5, 2025, 1:00pm UTC](https://gromacs.bioexcel.eu/t/my-production-file-periodic-boundary/11466 "2025-02-05T13:00:04Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![golbarg](https://avatars.discourse-cdn.com/v4/letter/g/c2a13f/32.png) [@golbarg](https://gromacs.bioexcel.eu/u/golbarg)\
**Post date:** [February 5, 2025, 1:00pm UTC](https://gromacs.bioexcel.eu/t/my-production-file-periodic-boundary/11466/1 "2025-02-05T13:00:04Z")

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GROMACS version: 2024.4  
GROMACS modification: Yes/No  
Hello,  
I made a coarse-grained membrane looking like the composition below:  
layer 1: water and ions  
layer 2: outer leaflet  
layer 3: inner leaflet  
layer 4: water and ions  
Then after neutralizing, minimizing, and equillibrating, ran my membrane for 10 microseconds with a 25 fs timestep.  
When I visualized it in VMD, I realized that layer 4 and half of layer 3 has crossed the periodic boundary and appeared and top so it looked like this:  
layer 3: half of the inner leaflet  
layer 4: water and ions  
layer 1: water and ions  
layer 2: outer leaflet  
layer 3: the other half of the inner leaflet

I used trjconv -pbc mol and -pbc whole on my membrane but it did not fix it and gave me the same outcome when I visualized it on VMD. I centered my membrane based on my system as well and still did not work. Are there any other ways to fix this?  
I am currently running a bigger membrane with more water (thought that maybe there was not enough water to keep them in place.

commands:

gmx trjconv -pbc mol -f production.xtc -s production.tpr -n file\_CG.ndx -o production-PBC1.xtc

gmx trjconv -pbc whole -f production.xtc -s production.tpr -n file\_CG.ndx -o production-PBC2.xtc

additionally, tried centering too while using pbc mol and whole

Thank you in advance!