Coalescence of the G13A Bundles Here, a POPC membrane (128 lipids) with an equilibrated wild- type bundle (consisting of 6 trans-membrane arranged peptides and 2 ‘bystander’ peptides) was copied in both the X and Y dimension. The G13A mutation was performed on this system. Both wild-type and G13A mutant simulations were run at 310 K. For the reverse simulation (G13A to wild-type) the final snapshot of the G13A simulation was taken, and the G13A mutation was restored to the wild-type. The peptide aggregation number of the largest bundle was calculated using a cluster algorithm. This algorithm clustered all back-bone atoms, which where located within +1.0 and 21.0 nm from the membrane center, based on a distance cutoff of 2.0 nm. Simulation Details The simulations described in this paper were performed with the GROMACS simulation package [74], version 4.0.5. We used the Martini model version 2.1 [28,29] to simulate the lipids and amino acids. 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Macromolecules 30: 3242–3255. PLoS ONE | www.plosone.org 13 June 2012 | Volume 7 | Issue 6 | e38302