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. Author manuscript; available in PMC: 2019 Jun 3.
Published in final edited form as: J Chem Theory Comput. 2018 Nov 29;14(12):6642–6652. doi: 10.1021/acs.jctc.8b00765

Figure 2. Area matching in BUMPy.

Figure 2.

1) An initial bilayer patch is larger than the required dimensions. 2) Slices of the original bilayer are taken separately by the top and bottom leaflets to match their specific area requirements, dependent on the requested geometry and zo location. 3) The top and bottom leaflets are scaled laterally to occupy the size corresponding to the requested geometry. At this point, the density of lipids in the top leaflet is higher than in the original bilayer, and the density in the bottom leaflet is lower than in the original bilayer. 4) The geometric transformation takes place.