Simulation pipeline for mu-opioid receptor in the lipid bilayer consisting of POPC molecules

In equilibration folder, you will find the several scripts, which are different steps of the simulation. The order of the files are explained in equilibration_protocol.txt.

In Production folder, there are scripts for 50 ns-long simulations in NPAT ensemble, with different restraints.

The scripts are supposed to run in Langevin Dynamics only, if the integrator is changed, the structure of the scripts should altered as well.