Area per Lipid from a Hexagonal box

[Thomas Evangelidis]

Hi,

I did my simulation in a hexagonal prism and calculated the Area per Lipid in: 1) the original trajectory, 2) after wrapping to an orthorhombic box and 3) after wrapping to a parallelepiped. The orthorhombic box yielded the closest to native fluctuations but wrapping a hexagon to an orthorhombic box is fundamentally wrong. Is there a trick to get correct Area per Lipid values from a hexagonal prism?

thanks in advance,
Thomas

[Ismael Rodriguez Espigares]

Unfortunately, the first release of MEMBPLUGIN only works with parallelepiped unit cells. Some of the tools which doesn't need wrapping such as SCD order and tilt angle might work. I don't know if there is any solution right now, but we will try to implement it on next releases.

Bests,
Ismael.

[Thomas Evangelidis]

Hi Ismael,

It would be very useful to be able to use MEMPLUGIN tools with hexagonal cells in the future. Apart from SCD, which other MEMPLUGIN tools do not require wrapping?

thanks,
Thomas

[Toni]

I don't believe VMD or pbctools themselves properly support hexagonal cells.

The tools work under the assumption that the system is wrapped (either by the user, or at runtime with the given command). Area per lipid and membrane thickness map definitely require this assumption.