Molecular dynamics simulations of the serotonin import process of the human serotonin transporter. Article link: https://doi.org/10.1016/j.bpj.2022.01.024. SeTWT-5HT-stripped.pdb - stripped (no lipids or water) topology file for SERT-5HT trajectories. MSM-SeTWT-5HT-500microstates-100samples.zip contains trajectory files of 100 structures of each microstates (500 total) from the SERT-5HT Markov state model in xtc format. SeTWT-Na-stripped.pdb - stripped (no lipids or water) topology file for SERT-Na (no substrate) trajectories. MSM-SeTWT-Na-600microstates-100samples.zip contains trajectory files of 100 structures of each microstates (600 total) from the SERT-Na Markov state model in xtc format. Trajectories may be viewed in molecular graphics software such as VMD. Residue numbering in the trajectories is offset by 75 from the original SERT sequence.