# Why membrane rupture durning the energy minimization?

**URL:** <https://gromacs.bioexcel.eu/t/why-membrane-rupture-durning-the-energy-minimization/9772>\
**Category:** User discussions\
**Tags:** energy-minization\
**Created:** [July 29, 2024, 3:24pm UTC](https://gromacs.bioexcel.eu/t/why-membrane-rupture-durning-the-energy-minimization/9772 "2024-07-29T15:24:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Fayaz](https://avatars.discourse-cdn.com/v4/letter/f/22d042/32.png) [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\
**Post date:** [July 29, 2024, 3:24pm UTC](https://gromacs.bioexcel.eu/t/why-membrane-rupture-durning-the-energy-minimization/9772/1 "2024-07-29T15:24:54Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
i am doing the md simulation of pure /mix membrane of phospholipids and glycolipids , i have attached the pbc box file its okay but when i am doing the energy minimization step my structure is broken how to fix this solution. i have attached both gmx gromp and minimization output

 ![em output](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e3f39b6f5fa866ef711e7a8faccfca6cb8bb571a.png)  
 ![pbc](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/52f8c53c853a6f7d26418e1ac25e22b999d00451.png)

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [July 29, 2024, 4:13pm UTC](https://gromacs.bioexcel.eu/t/why-membrane-rupture-durning-the-energy-minimization/9772/2 "2024-07-29T16:13:41Z")

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Is the box size correctly set? Can you visualize the box boundaries in your pre-minimization structure?

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<div class="post-metadata">

**Author:** ![Fayaz](https://avatars.discourse-cdn.com/v4/letter/f/22d042/32.png) [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\
**Post date:** [July 29, 2024, 4:20pm UTC](https://gromacs.bioexcel.eu/t/why-membrane-rupture-durning-the-energy-minimization/9772/3 "2024-07-29T16:20:02Z")

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yes sir the box is correctly set i used the commands  
gmx editconf -f KALP-15\_processed.gro -o KALP\_newbox.gro -c -box 9.50000 8.00000 8.00000 .Can u please tell me what does means of  
Can you visualize the box boundaries in your pre-minimization structure?