# Protein getting out of water box

**URL:** <https://gromacs.bioexcel.eu/t/protein-getting-out-of-water-box/1140>\
**Category:** User discussions\
**Created:** [November 22, 2020, 7:25pm UTC](https://gromacs.bioexcel.eu/t/protein-getting-out-of-water-box/1140 "2020-11-22T19:25:07Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![nadimferdous32](https://avatars.discourse-cdn.com/v4/letter/n/9d8465/32.png) [@nadimferdous32](https://gromacs.bioexcel.eu/u/nadimferdous32)\
**Post date:** [November 22, 2020, 7:25pm UTC](https://gromacs.bioexcel.eu/t/protein-getting-out-of-water-box/1140/1 "2020-11-22T19:25:07Z")

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GROMACS version: 2020.02  
GROMACS modification: Yes/No  
I have done a 500ns simulation of a protein (256aa) using Gromacs. While analyzing in VMD, I found that the protein gets slightly out of the box after 420ns. Also, the RMSD score seems to increase after about 350ns. Why is this happening?

I have used AMBER99SB-ILDN forcefield. Padding distance was 1.1 and box volume was 512 nm3.

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**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [November 23, 2020, 12:34am UTC](https://gromacs.bioexcel.eu/t/protein-getting-out-of-water-box/1140/2 "2020-11-23T00:34:45Z")

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Most likely [http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc](http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc)