# Protein is ejected out of box after MD simulation **URL:** \ **Category:** User discussions\ **Created:** [July 26, 2024, 3:39pm UTC](https://gromacs.bioexcel.eu/t/protein-is-ejected-out-of-box-after-md-simulation/9757 "2024-07-26T15:39:32Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [July 26, 2024, 3:39pm UTC](https://gromacs.bioexcel.eu/t/protein-is-ejected-out-of-box-after-md-simulation/9757/1 "2024-07-26T15:39:32Z")
GROMACS version: 2019 GROMACS modification: Yes/No Here post your question Hi guys, This is my problem when i run MD simulation. I have run MD simulation, however, when i check files: nvt.gro, npt.gro, md.gro, i see that protein is ejected out of the box and ligand also (like a picture that i sent below). Results of md.log, npt.log and nvt.log are normal and they completely finish. It would be great if you guys can tell me what is my problem and how to fix them. Thank you so much. Nhina. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/bc9308794406769de744377210479a88649429b8.jpeg) ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [July 26, 2024, 4:03pm UTC](https://gromacs.bioexcel.eu/t/protein-is-ejected-out-of-box-after-md-simulation/9757/2 "2024-07-26T16:03:14Z")
probably pbc issue- check out [gmx trjconv](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html) ---
**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Post date:** [July 27, 2024, 11:11am UTC](https://gromacs.bioexcel.eu/t/protein-is-ejected-out-of-box-after-md-simulation/9757/4 "2024-07-27T11:11:36Z")
i did it thank you very much