2026-10-13T07:19:44Z https://www.scidb.cn/oai

10.57760/sciencedb.39974 2026-06-23T00:27:15Z

2026-06-23 Associated data for: Molecular Dynamics Study of the Temperature Responsiveness of Cd²⁺ Ion and Its DNA Aptamer: Conformational Memory and Temperature Hysteresis doi:10.57760/sciencedb.39974 en The dataset is organized in the following structure:Root directory contains analysis scripts (e.g., FES_Analysis.py) and all processed data.Six subdirectories (Cd2+-DNA-aptamer-Id-seed23451 to -23456) contain per-seed simulation outputs:Trajectory: md_0_1_center.xtc (post-PBC corrected, 500 ns, saved every 10 ps).Topology: topol.top, *.gro, *.itp (AMBER99SB-ILDN for DNA, custom LJ parameters for Cd²⁺ [0]).Processed data: dist_cd_dna.xvg (Cd²⁺-DNA minimum distance), num_contacts.xvg (contact count), rmsd_backbone.xvg (backbone RMSD).Representative PDBs: Binding, dissociation, and rebinding phase snapshots.File formats: .xtc (trajectory), .xvg (numerical time series, readable by Grace/mdanalysis), .gro/.pdb (coordinates), .py (Python 3.9+). All time series use consistent column layout: time in first column (ns), value in second. Detailed file descriptions are provided in the README.txt within each subdirectory. Cadmium ion; DNA aptamer; Molecular dynamics simulation; Conformational memory; Temperature hysteresis; Coordination switching Lingfeng Jiang PUBLIC https://creativecommons.org/licenses/by-nc-nd/4.0/ dataset Science Data Bank