[gmx-users] Orientation of protein

[Shima Arasteh]

Dear users,

As a matter of fact I don't know the exact orientation of my protein. To insert a protein in a lipid bilayer, I need to set the orientation of protein and bilayer parallel to z-axis. I'd like to know if it is necessary for protein to be in z-direction exactly? Is it acceptable to set the protein's direction approximately?  


Thanks in advance.
Sincerely,
Shima