Molecular dynamics trajectories of apomyoglobin at pH 4

Dataset This dataset contains molecular dynamics trajectories of apomyoglobin simulated at pH 4 on NCSA Blue Waters using GROMACS 5.0.4. At pH 4.0, all GLU and ASP sidechains are unprotonated (with -1 charge) and all HIS sidechains are (doubly) protonated (with +1 charge). See the README.md for a description of the full dataset, only a subset if represented here. Nine replicates (run1 thru run9) of restrained simulations to encourage local unfolding… each at 6 different temperatures (300K, 330K, 350K, 370K, 400K, 415K) …and at each temperature different restraint strengths (k0.1 k0.2 k0.3 k0.4 k0.5 k0.6 k0.7 k0.8 k0.9 k1.0 k1.1 k1.2 k1.5) Trajectories are about 760 ns in length: traj.xtc files - compressed protein coords (no solvent) saved every 100 ps Contents README.md - a description of the full dataset (available) upon requection confout.gro - GROMACS structure of apomyoglobin with full solvent confout_protein_only.gro - GROMACS structure of apomyoglobin only (use to visualize/analyze xtc files) index.ndx - GROMACS index file defining atom groups Archives of trajectory data: run1.tar.gz - archive of trajectory data (with trr files removed) run2.tar.gz - archive of trajectory data (with trr files removed) run3.tar.gz - archive of trajectory data (with trr files removed) run4.tar.gz - archive of trajectory data (with trr files removed) run5.tar.gz - archive of trajectory data (with trr files removed) run6.tar.gz - archive of trajectory data (with trr files removed) run7.tar.gz - archive of trajectory data (with trr files removed) run8.tar.gz - archive of trajectory data (with trr files removed) tprs.tar.gz - archive of GROMACS binary *.tpr files for simulation (545 MB) scripts.tar.gz - archive of scripts used for preparing and running simulation make_whole.py mcopy.py mm.py NOTE qsub.sh reduce_trr.py submit_all submit_all_runs submit_all_runs.py Citation Wan, Hongbin, Yunhui Ge, Asghar Razavi, and Vincent A. Voelz. "Reconciling simulated ensembles of apomyoglobin with experimental hydrogen/deuterium exchange data using bayesian inference and multiensemble markov state models." Journal of chemical theory and computation 16, no. 2 (2020): 1333-1348. DOI: https://doi.org/10.1021/acs.jctc.9b01240