1. The protein should be first embedded into the bilayer. (The center of bilayer at the plane z = 0)

If you have the pdb id, you can download the embedded protein from Orientations of Proteins in Membranes (OPM) database. (https://opm.phar.umich.edu)

If you have you own protein, you can use the PPM SERVER which can embed your protein relative to the membrane bilayer. (https://opm.phar.umich.edu/ppm_server)

2. Generate the simulation folder.

For example: python ~/openawsem/mm_create_project.py 6w5s.pdb --hybrid

You can also let it to generate frag memory by add option "--frag" which will take a while.

3. Tell the program that what potentials to use by Modifying the force_setup.py file

The potentials can be turn on and off by commenting and uncommenting the potential function.

To simulate a protein both globular and membrane part:

comment "contact_term(oa),".

uncomment "contact_term(oa, z_dependent=True, inMembrane=True, membrane_center=membrane_center, k_relative_mem=3),"

uncomment "membrane_term(oa, k=1*kilocalorie_per_mole, membrane_center=membrane_center),"

You can specify the potential to be used, or write your own potential and include them here.

4. Run the simulation

For example: "python mm_run.py 6w5s --to test -s 1e3 -r 100 --tempStart 300"