Input and start files, parameters for REMD simulations in article 'Allosteric Ensembles Elucidate Mechanisms of Inhibition in the Human Soluble Epoxide Hydrolase'

Overview The Replicate Exchange Molecular Dynamics (REMD) simulation was run on GROMACS (2021.3) using AMBER ff14SB force field. (Ligand was parameterized wth General AMBER Force Field and partial charges were calculated using AM1-BCC method.) Description start_input_files.zip The start and input files for simulation system Apo (control), PTG423 and PTG522. /s1-s25 folders corresponding to the 25 replicas with temperatures evenly spaced between 299.0 and 340.13 K. Each replica folder contains: File Description eqp300.gro The relaxed starting structure for simulation posre*.itp Position-restraining files *.ndx Index file *.mdp Input file of the final equilibration step *_md_0_1.tpr Start file of the first 10 ns simulation *.top Topology file all_mdp_input_eq.zip All mdp files for energy minimization and equilibration.