# Simulation box broken

**URL:** <https://gromacs.bioexcel.eu/t/simulation-box-broken/11705>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [March 10, 2025, 6:57am UTC](https://gromacs.bioexcel.eu/t/simulation-box-broken/11705 "2025-03-10T06:57:07Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![nilanjana88](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@nilanjana88](https://gromacs.bioexcel.eu/u/nilanjana88)\
**Post date:** [March 10, 2025, 6:57am UTC](https://gromacs.bioexcel.eu/t/simulation-box-broken/11705/1 "2025-03-10T06:57:07Z")

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GROMACS version: 2024.2  
GROMACS modification: No

Hello,  
I am facing a problem with protein-ligand simulation box created using the standard tutorial. The “.gro” file created during the last step looks like weird when loaded in VMD.

 ![Screenshot from 2025-03-10 12-20-59](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/6b3bac5274a01a1461770b0370f929b4b77a45a4.png)  
Seems like, the simulation box is broken at few areas, and complex is also not compact.

I have performed quite a many simulation before, and never faced any issues like a broken simulation box.

Although after I centered the XTC file, visualized them again in VMD, it looked fine; and got RMSD values in expected range, but the GRO file scares me.  
Is it common? Or did make any mistakes during the setup?

I remember getting some warning in NPT and NVT equillibration steps saying. “**WARNING 2 [file topol.top, line 53735]:**  
\*\* Too few parameters on line (source file\*\*  
\*\* /home/Desktop/GROMACS/gromacs-2024.2/src/gromacs/gmxpreprocess/toppush.cpp,\*\*  
\*\* line 1899)\*\*”.  
But was not sure what might have gone wrong, so had overwritten it with “maxwarn 2”.

Any help would be highly appreciated.  
Thank you!