This record contains additional input files for the simulations carried out for the publication:David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, and Gary Tresadern, Current state of open source force fields in protein-ligand binding affinity predictions, 2024. Folder Content gromacs_input Input Gromacs[1] mdp files for the following simulations at states A and B, respectively: energy minimization (em), NVT equilibration (nvt), NPT production (npt) and non equilibrium simulaations (morphes). protein_parameters Protein force field parameters for the forcefild Amber99sb*-ILDN [2] workflow_scripts Example workflow scripts which were used to prepare, run, and analyze the simulations. To run these scripts, pmx (https://github.com/dfhahn/pmx)[3] and the Open Force Field toolkit, release 0.8.4.[4] [1] Abraham, M.; Alekseenko, A.; Bergh, C.; Blau, C.; Briand, E.; Doijade, M.; Fleischmann, S.; Gapsys, V.; Gaurav Garg,; Gorelov, S.; Gouaillardet, G.; Gray, A.; M. Eric Irrgang,; Jalalypour, F.; Jordan, J.; Junghans, C.; Prashanth Kanduri,; Keller, S.; Kutzner, C.; Lemkul, J. A.; Lundborg, M.; Merz, P.; Mileti ́c, V.; Morozov, D.; P ́all, S.; Schulz, R.; Shirts, M.; Shvetsov, A.; Soproni, B.; Van Der Spoel, D.; Turner, P.; Uphoff, C.; Villa, A.; Wingberm ̈uhle, S.; Zhmurov, A.; Bauer, P.; Hess, B.; Lindahl, E. GROMACS 2023.2 Manual. 2023, Publisher: Zenodo Version Number: 2023.2. [2] Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field. Proteins 2010, 78, 1950–1958. [3] Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L. pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comp. Chem. 2015, 36, 348–354. [4] Wagner, J.; Mobley, D. L.; Thompson, M.; Bannan, C.; Chodera, J.; Rizzi, A.; Gokey, T.,; Dotson, D.; Rodrıguez-Guerra, J.; Camila,; Bayly, C.; Horton, J; Behara, P.; Lim, N. M.; Boothroyd, S.; Lim, V.; Sasmal, S.; Smith, D.; Wang, L.-P.; Zhao, Y. openforcefield/openforcefield: 0.8.3 Major bugfix release. 2021; https://zenodo.org/record/4429313