Lindex.py- Calculates Lindemann index. Requires pandas and Plumed installed. Caparotta, M., Bustos, D. M., & Masone, D. (2020). Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature. Physical Chemistry Chemical Physics, 22(9), 5255-5263.bead_count.py- Count C4B beads between bilayers (see paper for more details). Requires numpy and MDAnalysis. Caparotta, M., Tomes, C. N., Mayorga, L. S., & Masone, D. (2020). The synaptotagmin-1 c2b domain is a key regulator in the stabilization of the fusion pore. Journal of Chemical Theory and Computation, 16(12), 7840-7851.pore_distance.py- Measure the distance between an SMA copolymer and the center of the fusion pore. Requires numpy and MDAnalysis. Caparotta, M., Puiatti, M., & Masone, D. (2021). Artificial stabilization of the fusion pore by intra-organelle styrene–maleic acid copolymers. Soft Matter, 17(36), 8314-8321.