I hesitate to use MERGE COOR RECENTER, since the the protein will be shifted in z as well as x and y, which may not be desirable. Also, if (1) the bilayer remains centered around z=0 during the simulation, and (2) the distance between the protein an bilayer surface is variable, you may wish to use a fixed point in z instead of ?ZAVE, which is the center of the protein. If the protein is always above (+z) the bilayer, ?ZMIN is a better choice as well. For the x,y shift--

traj read
coor stat sele segid prot end
coor tran xdir -?XAVE ydir -?YAVE
update imgfrq 1 ...
define lipunder sele segi lipi .and. point 0. 0. ?ZAVE CUT 15 end

Rick Venable
computational chemist