[gmx-users] PMF ligand membrane protein

[nahren manuel]

Dear Gromacs User,
this is the first time I am attempting membrane protein simulation.
I wish to obtain a PMF value for a ligand permeating through a membrane protein (lacY permease). In the Xray str. the ligand is almost at the center of the protein. I wish to generate enough initial configurations (using N N Y, along 'z' axis) prior to starting umbrella sampling. the ligand of course is being pulled, but which part should I keep as reference (or should I look for another alternative). I was thinking of pull_geometry = reference, but since this option has been left out in GMX 5.1.4, I do not know what to keep as the reference. Some assistance on how to proceed would be helpful. 
Thanks.
Best,nahren