[gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

Shay Amram shayamra at post.tau.ac.il
Wed Jun 3 00:17:08 CEST 2009

Dear GROMACS users,


I have been trying to expand a membrane by a non-integer multiplier (for
example X1.5). This can be done using


genbox -cs Membrane.gro -o Expanded_membrane.gro -box 1.5X 1.5Y Z


This has worked very good with homogenous membranes, and only very short
equilibrium times were required to re-equilibrate the membrane (~10-20ns).

Now I am trying to deal the same way with heterogeneous membrane (POPG/POPE
mixture, Mikko Karttunen et. al). 


When trying to invoke the above command to the POPG/POPE membrane I get a
membrane with different compositions of lipids in the upper and lower

This happens (so I suspect) because the arrangement of lipids in each
leaflet is somewhat different so that the molecules that "get' to be
multiplied do not conserve the 

same ratio of different lipids as in the original structure (which has ratio
of 1:3 POPG/POPE).


Is there a way to multiply the membrane by a non-integer number AND somehow
conserve the ratio of different lipid species too?

Or at the very least, to have both upper and lower leaflets identical after
multiplication? (This, too, would help immensely).






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