[gmx-users] PBC correction to visualize a protein-membrane structure

[Juan Munoz-Garcia]

Dear GROMACS users,

I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I still get the same structure. Even more weird is that when I turn on the periodic images option in vmd I still don’t see the right protein embedded into the lipid bilayer. As this can’t be a real effect of minimisation, I'd like to ask you for advice.

Thank you.
Juan C. Munoz-Garcia

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