lipid-wrap.tcl​:
# script to wrap lipid (and protein) system to make a centered trajectory
# Somehow, this doesn't work with mixed bilayers. The selection "lipid" only selects POPC, not POPS.

# call the pbc tools plugin
package require pbctools

# wrap the lipid bilayer around the center of mass of the protein
pbc wrap -all -sel "lipid" -compound res -center com -centersel "protein"

# now, wrap the solvent & ions around the wrapped complex of protein and lipids
pbc wrap -all -sel "water or ions" -compound res -center com -centersel "protein or lipid"

# center each frame of the trajectory so that is it aligned at the origin (0,0,0)
set nf [molinfo top get numframes]
set all [atomselect top all]
for {set i 0} {$i < $nf} {incr i 1} {
    animate goto $i
    $all moveby [vecinvert [measure center $all]]
}