[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Christopher Neale]

Dear David:

If the two leaflets are moving with respect to each other (along the bilayer plane), then why would this be artificial? 
I have also seen this (diffusive) motion, and in addition to wondering why you would call it artificial, it seems to me 
that the motion would have to be many orders of magnitude larger than is observed
in simulations for it to affect the temperature.
Subtracting the COM of each leaflet separately is not only impossible, but inadvisable.

Chris.

-- original message --

I ran into similar issues for a DPPC bilayer. It might be possible
that the two leaflets of the bilayer are moving with respect to
eachother. If this is not taken into account, these artificial
velocities will mean the simulation thinks it is at a higher
temperature than it really is. If possible, you might want to try
subtracting the center of mass motion of each leaflet, rather than the
center of mass motion of the entire bilayer. This will allow the
system to equillibrate to the correct (higher) temperature, and should
increase the area per lipid of the bilayer.

Hope this helps.
-David