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 leaflets. 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). Thanks, -Shay
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