I have performed a lipid membrane simulation only in NAMD using PBC, then used this command to wrap the trajectory (pbc wrap -center bb -centersel membplugin_lipid -compound res -all) the command was taken from the MEMBPLUGIN in VMD which is done before doing some analyses such as membrane thickness or area per lipid. But when i tried to align the trajectory in VMD (using the RMSD trajectory tool) after wrapping it, (aligning was done on all with noh selected) some of the frames showed large motions (image attached).

the reason i want to align is that after wrapping, i found that the membrane itselft move up and down in the Z axis inside the simulation box. i think the analyses should be performed after aligning on the first frame (i dont know whether this is correct or not).

So how can i align without this large motion?

Thanks