Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method 
Ming Huang, Wenjun Huang, Fei Wen, and Ronald G. Larson*
Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136
*rlarson@umich.edu


Parameters Used in the Umbrella Sampling Simulations

We provide the parameters used in Umbrella Sampling simulations carried using GROMACS 4.6.5 reported in our study (DOI: 10.1002/jcc.24845), namely the set positions (x) and spring constants (K) for each window in simulations. Tab 1 lists the names of the peptides and their corresponding sequences. Tab 2-12 lists the parameters. The title of each simulation in Tab 2-12 follows the convention ˇ°Force Field_Peptide Name_Reaction Coordinateˇ±. Note two reaction coordinates are employer, namely center-of-mass (COM) and peeling from one peptide end (peel). Those marked with ˇ°*ˇ± are windows repaired by increasing the spring constant; those marked with ˇ°**ˇ± are windows added to ensure sufficient overlap, where overlap was inadequate in the original histograms. These parameters can be supplied to GROMACS 4.6.5 via the following commends in mdp file: pull: umbrella; pull-geometry: distance; pull-coord1-init: set_distance_in_table; pull-coord1-k: K_value_in_table;