[gmx-users] Inverting PBC for membrane simulations

Alan Dodd anoddlad at yahoo.com
Mon Dec 13 14:15:46 CET 2004

As there is a potential surface tension difference
between the two leaflets of the bilayer in my
simulation,  I would like to be able to modify the
periodic boundary conditions such that the z axis is
inverted in the xy neighboring cells (by rotating
about the xy diagonal) - so a lipid can diffuse out of
the top leaflet and into the bottom leaflet at the
edges of the box.  I know of an example where similar
things have been done before, but not with Gromacs. 
Are there any ways in which this can be done?

Alan Dodd
University of Bristol

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