# Remove translation into xy axis protein into membrane

**URL:** <https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748>\
**Category:** User discussions\
**Tags:** mdp-parameters\
**Created:** [August 28, 2021, 12:19am UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748 "2021-08-28T00:19:19Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![groponp](https://avatars.discourse-cdn.com/v4/letter/g/258eb7/32.png) [@groponp](https://gromacs.bioexcel.eu/u/groponp)\
**Post date:** [August 28, 2021, 12:19am UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748/1 "2021-08-28T00:19:19Z")

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Dear user,

Dear users,

I have a membrane protein that I want to prevent from being translated along the x and y axis, in NAMD I can do this with dummy atoms, and a force of 2.5 kcal / mol, this without affecting its functions (conformational changes and / or transport ), however I don’t know how to do this with GROMACS, since I am running COARSE-GRINED simulations, please if someone can tell me.

PS: Maybe the cylinder restrain could help me, but I don’t know how to add these parameters to the gromacs config file

Better,

Geo.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [August 30, 2021, 9:18am UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748/2 "2021-08-30T09:18:08Z")

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Why do you need a restraint? Translational diffusion doesn’t affect anything and can be corrected after the simulation using `gmx trjconv`.

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**Author:** ![groponp](https://avatars.discourse-cdn.com/v4/letter/g/258eb7/32.png) [@groponp](https://gromacs.bioexcel.eu/u/groponp)\
**Post date:** [August 30, 2021, 2:54pm UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748/3 "2021-08-30T14:54:26Z")

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You can give me . In good example to remove long translation protein into membrane XY component using trjconv?

Best,

Geo.

Obtener [Outlook para iOS](https://aka.ms/o0ukef)

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 1, 2021, 10:18am UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748/4 "2021-09-01T10:18:41Z")

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See the available options for that can be supplied to `-fit`. There are several specifically designed to remove XY rotation and translation for exactly this case.

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**Author:** ![groponp](https://avatars.discourse-cdn.com/v4/letter/g/258eb7/32.png) [@groponp](https://gromacs.bioexcel.eu/u/groponp)\
**Post date:** [September 1, 2021, 4:27pm UTC](https://gromacs.bioexcel.eu/t/remove-translation-into-xy-axis-protein-into-membrane/2748/5 "2021-09-01T16:27:03Z")

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Thanks so much.

Geo.

Obtener [Outlook para iOS](https://aka.ms/o0ukef)