# Box explodes using NPT.mdp

**URL:** <https://gromacs.bioexcel.eu/t/box-explodes-using-npt-mdp/12977>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, simulation-setup\
**Created:** [November 25, 2025, 8:10pm UTC](https://gromacs.bioexcel.eu/t/box-explodes-using-npt-mdp/12977 "2025-11-25T20:10:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![gluizcar](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@gluizcar](https://gromacs.bioexcel.eu/u/gluizcar)\
**Post date:** [November 25, 2025, 8:10pm UTC](https://gromacs.bioexcel.eu/t/box-explodes-using-npt-mdp/12977/1 "2025-11-25T20:10:52Z")

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GROMACS version: 2022  
GROMACS modification: No  
I performed a simulation (equilibration) with a Janus MoSSe box containing ions and water. However, my box explodes when I use NPT.mdp. I’m attaching the mdp inputs regarding 1-optimize (equilibration) and 2-NPT and along with some screenshots of the simulation visualization: 01 = when it starts, 02 = the box decrease, and 03 and 04 the box explodes. Could someone help, or suggest a way to fix this problem?

 ![04](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c581e49de811d787595d9a1b5fd320f512a0f862.jpeg)

 ![03](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/936dc697e563e3ce3c138cbc1c579d4d9e59878d.jpeg)

 ![02](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e59e77e6435f13f414f60b64ced6f54de62de4bd.jpeg)

 ![01](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/d5b5ba05b0cfa44ed22c9a40ff8121bb8f75e6e5.jpeg)

[1-optmize.mdp](https://gromacs.bioexcel.eu/uploads/short-url/uq4g42tIo8cFPI4Va34zw6PivO1.mdp) (1.7 KB)

[2-NPT.mdp](https://gromacs.bioexcel.eu/uploads/short-url/o9LpSFi3cgiYPZbEMvNLFawMtk3.mdp) (3.8 KB)

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [November 25, 2025, 8:41pm UTC](https://gromacs.bioexcel.eu/t/box-explodes-using-npt-mdp/12977/2 "2025-11-25T20:41:46Z")

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Hi, I would suggest using c-rescale and possibly reduce the compressibility by a factor of 10, at least in the equilibration phase. I think you can use a semiisotropic scaling instead of anisotropic for your setup.

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 26, 2025, 7:40am UTC](https://gromacs.bioexcel.eu/t/box-explodes-using-npt-mdp/12977/3 "2025-11-26T07:40:09Z")

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Note that frozen atoms cause issues with the pressure calculation. I don’t know how large the effect is in your system, but this could make pressure coupling impossible to use.