Remove translation into xy axis protein into membrane

User discussions
1

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.

2

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

3

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

Best,

Geo.

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4

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.

5

Thanks so much.

Geo.

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