Simulation trajectories for: How sensitive are protein hydration shells to electrolyte concentration and protein composition?

PROJECT DESCRIPTION:We used classical, atomistic molecular dynamics simulations to investigate the hydrogen bond structure of the solvation shells of 5 halophilic and 5 mesophilic proteins in low (0.15 mol/kg) and high (2 mol/kg) aqueous KCl solutions. The simulation results reveal that, despite systematic amino acid composition differences between these two types of proteins, the hydrogen bond structure in their solvation shells is similarly robust to changes in KCl concentration.

DATASET DESCRIPTION:This dataset contains 15 of the 20 production run simulation trajectories  mentioned in the indicated related publication:- proteins 1DOI-1FRD  at both KCl concentrations (proteins are identified by their pdb ID, given in the order "halophile-mesophile");- proteins 1V9E-4CNX at both KCl concentrations; - proteins 1HZ6-2KAC at both KCl concentrations;- protein 2L28 at 2 molal KCl (halophile)- protein 2ITH at both KCl concentrations (mesophile).  

Single copies of each of the simulated proteins were simulated immersed in 0.15 molal and 2 molal aqueous KCl solutions, using TIP3P water, the AMBER99SB force field for the proteins, Joung and Cheatham parameters for the ions, and modified Lennard-Jones for interactions involving carboxylate oxygens (Geraili and Vila Verde, Biophysical Journal, Volume 120, Issue 13, 2746 - 2762, and   Kashefolgheta and Vila Verde, Phys. Chem. Chem. Phys., 2017, 19, 20593-20607)

USAGE: unzip all files from the same directory, so the directory trees are preserved.Please note, that some Microsoft Windows Installations encounter some errors while extracting the zip archives due to their depth of directories. Tools like 7zip are able to extract these directories on MS Windows.

Base directory structure:     /homes/adj781h/geraili/Ph.D._Project/001.0_Protein_folding_problem/002.0_impact_of_acidic_amino_acids/003.2_Dynamics/Dynamics/'\$molecule'/'\$conc'/'\$typ'/Protein_dynamics/Run    where     - \$molecule is one of 1DOI_1FRD  1HZ6_2KAC  1V9E_4CNX 2L28_2ITH (each of the halophilic/mesophilic protein pairs)    - \$conc is either 2molal or 0.15molal and denots the KCl concentration in the aqueous solvent    - \$typ is either Halophile or Non-Halophile

RELATED DATASET: Other simulation input and other output files for the same simulations can be found in https://doi.org/10.17877/RESOLV-2024-m32ubdo9. To use these datasets together, place all *zip files in the same directory and unzip them. The directory structure will be preserved, so it will be easy to identify which input files gave origin to each trajectory.