Dataset 3 for paper "Electric Field-Induced Destabilization and Surface Modulation of Aβ42 Fibrils in Molecular Simulations"

Database contains: starting configuration for simulations: conf.gro mdp for reproducing simulation: 3-pr-npt.mdp positional restraint file: posre.itp example topology tpr: md.tpr topology file: topol.top protein topology file of the restrained protein: topol_Protein_chain_a.itp protein topology file of the unrestrained protein: topol_Protein_chain_a_free.itp index file "r11-42_c25,26,27,28.ndx" for layer-wise analyses: Protein_chain25_&_r_11-42: the first monomer of the second layer, including only the core residues Protein_chain26_&_r_11-42: the second monomer of the second layer, including only the core residues Protein_chain27_&_r_11-42: the first monomer of the first (top) layer, including only the core residues Protein_chain28_&_r_11-42: the first monomer of the first (top) layer, including only the core residues lower_layer_&_r_11-42: the core of the second layer (combination of Protein_chain25_&_r_11-42 and Protein_chain25_&_r_11-42) upper_layer_&_r_11-42 the core of the first (top) layer (combination of Protein_chain27_&_r_11-42 and Protein_chain28_&_r_11-42) index file "r09-42_c25,26,27,28.ndx" as above but with different range of residues des-amber force field: des-amber.ff simulation trajectories as triplicates for electric field 0.08 V/nm. All directories contain the trajectory as md.xtc.