You'd have found it if you'd bothered searching literature.

What are the questions you intended to answer with your calculations?

Annemarie Honegger

Thanks for taking time to answer my question.

I want to check 1.insertion depth of my protein inside the membrane 2. Interactions between the protein and the cholesterol 3.The dynamics of my protein inside the membrane.

Dear Kimia

Using the Gromacs makes it much easier, and you can follow the steps from the tutorial presented.

Just follow the steps.

http://www.mdtutorials.com/gmx/membrane_protein/index.html