# Protein rotating in triclinic box

**URL:** <https://gromacs.bioexcel.eu/t/protein-rotating-in-triclinic-box/96>\
**Category:** User discussions\
**Created:** [May 9, 2020, 8:49am UTC](https://gromacs.bioexcel.eu/t/protein-rotating-in-triclinic-box/96 "2020-05-09T08:49:47Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![soumadwip](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@soumadwip](https://gromacs.bioexcel.eu/u/soumadwip)\
**Post date:** [May 9, 2020, 8:49am UTC](https://gromacs.bioexcel.eu/t/protein-rotating-in-triclinic-box/96/1 "2020-05-09T08:49:47Z")

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Hi,

I have simulated a protein inside a triclinic box since it was computationally less expensive. During MD I see the protein coming out of the box and rotating. What’s more important is that I also see that its periodic image at a distance of 17 angstrom in the beginning of MD but the distance between these two images becoming ~10 angstrom at the end of the simulation. Is this usual or the choice of the triclinic box is not correct?  
Is the triclinic box so short in the z axis that the protein is interacting with its periodic image? If it is so, do you think this simulation will have artifacts? NB: I used -c -d 1.0 -bt triclinic option during gmx editconf.

Any suggestion will be appreciated.

Thank you in advance,  
Soumadwip Ghosh

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [May 11, 2020, 9:16am UTC](https://gromacs.bioexcel.eu/t/protein-rotating-in-triclinic-box/96/2 "2020-05-11T09:16:02Z")

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Hi,

Your system will most definitely have artifacts if your protein interacts with itself; I would suggest making sure that your keep a minimum distance of 1.2 nm as this is common setting for the vdW cut-off for common force-fields.

It’s useful if you check the distance to the next perodic image of the protein using `gmx mindist -pi`. The only option then is to run the simulation again and increase the `-d` parameter in `editconf`.

Regarding your setup:

If you use only -bt triclinic without any further input options, you will just get a rectangular box, because editconf will still use the default parameters for the box angles. Any box is triclinic, it’s the most general box-category which includes rectangular, octahedral, etc. boxes.

For all cases where a protein freely moves in water, you would like to use a box that is as spherical as possible, which is achieved by using the rhombic dodecahedron with `-bt dodecahedron` .

Find more information on how to set up the simulation boxes here:  
[http://manual.gromacs.org/current/reference-manual/algorithms/periodic-boundary-conditions.html](http://manual.gromacs.org/current/reference-manual/algorithms/periodic-boundary-conditions.html)

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [May 11, 2020, 9:23am UTC](https://gromacs.bioexcel.eu/t/protein-rotating-in-triclinic-box/96/3 "2020-05-11T09:23:49Z")

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Hi,  
The change in the minimum distance may be due to conformational change taking place in the protein during the simulation (e.i proteins can go from a more compact form to a more extended form, and that causes a reduction of the minimum distance). Did you try to visualise the protein before and after the simulation? Did you use GROMACS tools to calculate the minimum distance?

I do not see any issues with the options you use for gmx editconf.

Best regards  
Alessandra