# Ligand jumping from the box

**URL:** <https://gromacs.bioexcel.eu/t/ligand-jumping-from-the-box/12851>\
**Category:** User discussions\
**Tags:** gmx-grompp\
**Created:** [October 30, 2025, 11:42am UTC](https://gromacs.bioexcel.eu/t/ligand-jumping-from-the-box/12851 "2025-10-30T11:42:43Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Mashi](https://avatars.discourse-cdn.com/v4/letter/m/b4bc9f/32.png) [@Mashi](https://gromacs.bioexcel.eu/u/Mashi)\
**Post date:** [October 30, 2025, 11:42am UTC](https://gromacs.bioexcel.eu/t/ligand-jumping-from-the-box/12851/1 "2025-10-30T11:42:43Z")

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I have started the MD simulation of a protein ligand interaction for 100ns. first, i created a box for the protein in center then added the ligand molecules and after the neutralization, i saw all of my protein, ligand and water molecules were inside the box but after running the simulation i found that the ligand and water molecules are outside the box only protein is there in the center of the box. please help me how to solve this problem.