Input files and final structures (after 1 microsecond) of simulations of Mcl-1, Bax, and Bok transmembrane domains (TMDs) in a POPC membrane. CHARMM36 parameters are used for lipids and proteins and the CHARMM-specific TIP3P model for water. The systems were set up using CHARMM-GUI, and simualted using GROMACS with the simulation parameters recommended for CHARMM (see md.mdp). The simulations are described in detail in the paper [1]. Briefly, the final structures, given as .gro files here, were coarse-grained and used in high-throughput dimerization analyses. The dimer structures were clustered, and the most promising structures were fine-grained, and their stability was evaluated using atomistic simulations. [1] ADD