Molecular Dynamics Simulations of a Manganese Riboswitch

This dataset contains molecular dynamics simulations, input files, topologies and other necessary data supporting the study: pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal-sensing The simulations characterize the impact of pH-dependency on the conformational stability of the alx aptamer. Folder organization for standard MD is as follows: Native-Deprot 1-Prep-min 2-Initialization 3-MD 4-Steered Wobble-Prot 1-Prep-min 2-Initialization 3-MD 4-Steered 5-Equil 6-Post-Steered Within each sub-directory, there is a .zip file for each chain [A-D]. The contents are: Input files used for standard MD (i.e. topologies, mdp, gros, scripts) Processed trajectories (.xtc) for each chain and replicate (~1000-2000 frames) Similarly, the CpHMD folders are partitioned into Wobble-CpHMD and Native-CpHMD. Within each folder, there is a .zip for each chain [A-D] containing: Protonation data (.occ) for the titrable A92 residue Final .gro for each simulation Processed trajectories (.xtc) for each chain and replicate (~1000-2000 frames) Topologies found in the Native-Deprot and Wobble-Prot can be used with their respective CpHMD data. Additionally, a jupyter notebook is available to reproduce the plots found in the paper with the necessary data available. All simulations were performed using GROMACS 2022.3 with a modified OL3 RNA force field compatible with pH titration at 310K and 1 bar. Other relevant data is available on GitHub.