The actual displacements of particles constrained to move on a surface are best described using geodesic distances d(r i (t 2 ), r i (t 1 )), where r i (t) denotes the position of the i -th particle at time t. Geodesic distances can be efficiently computed on mesh surfaces using specialized methods, even without explicitly storing or constructing the corresponding shortest path. One such algorithm is the Vertex-oriented Triangle Propagation (VTP) of Qin et al. that simultaneously computes all distances from a source vertex to all other vertices on the mesh. Therefore, as the first step of our approach, we create a triangular mesh surface from each of the leaflets of the simulated membranes, using the center of mass of the lipid as a proxy for the center of diffusion. Then, we use the position of the closest vertex as an approximation of the true surface position of the lipid center of mass. For sufficiently fine