This repository contains the molecular dynamics simulation of the Na⁺/I^- symporter (NIS) ions-bound form described in Ravera et al. (2022), and includes the MD trajectories of only protein atoms and ions sampled every 100 ps, the python 3.8 Jupyter notebook used in the calculations reported and its required auxiliary files. The MD simulation was carried out using the cryoEM structure (2 Na⁺/I^- )-bound NIS embedded in a pre-equilibrated 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer. We obtained the parameters and scripts for the minimization, equilibration, and production using the molecular dynamics program GROMACS with scripts generated by the CHARMM-GUI web-server. The simulation was carried out with GROMACS, version 2020, in conjunction with the CharMM36 force field, using a TIP3P water model, Berger-derived DOPC lipids, and ion parameters by Joung and Cheatham (2008). Van der Waals interactions were cut off at 1 nm, and electrostatics were treated by PME beyond 1 nm. Temperature and pressure were kept at 310.5 K and 1 bar using the V-Rescale thermostat and Parrinello-Rahman barostat, respectively. All bonds were restrained using LINCS, and an integration time step of 2 fs was used. We energy-minimized (steepest descent)the experimental structure using a double-precision version of GROMACS, and performed a six steps (125, 125, 125, 500, 500, and 500 ns) of position restraint equilibration dynamics with a gradually lifted harmonic force constant (Fc) with different values of Fc for backbone atoms (100000, 2000, 1000, 500, 200, and 50 kJ/mol/nm²), side-chain atoms (2000, 2000, 1000, 500, 200, 50, and 0 kJ/mol/nm²), residue dihedrals (1000, 200, 200, 100, and kJ/mol/nm²), and lipids (1000, 400, 400, 200, 40, and 0 kJ/mol/nm²). Van der Waals parameters for I^- were taken from Li et al.( 2015).