Data and Analysis Scripts for "Salt-Independent Counterion Kinetics and Sub-Poisson Number Fluctuations in B-DNA from Microsecond Molecular Dynamics"

This dataset accompanies the publication "Salt-Independent Counterion Kineticsand Sub-Poisson Number Fluctuations in B-DNA from Microsecond MolecularDynamics" by Masato Tanigawa and Takafumi Iwaki, published in The Journal ofChemical Physics (2026, manuscript JCP26-AR-01080R). It contains the AMBER input files, molecular dynamics topology files (.prmtop),processed analysis results, and Python analysis scripts used in the study. Theresearch analyzed 29 independent 1-microsecond MD trajectories of three B-DNAstructures (PDB: 1BNA, 5DNB, 1NAJ) at ionic strengths from 0 to 521 mM NaCl totest the kinetic implications of Manning counterion condensation theory. Contents:- 01_md_input_files/ AMBER input files (min/nvt/npt/prod.in, tleap scripts)- 02_topologies/ AMBER .prmtop topology files for all 16 systems- 03_kww_fit_results/ KWW survival-function fit results for 29 simulations (fit_summary.json and S(t) data files)- 04_mfpt_analysis/ MFPT event analysis results for 5DNB- 05_analysis_scripts/ Python analysis scripts (ion residence, MFPT, autocorrelation, data compilation, figure generation)- 06_compiled_data/ Unified compiled dataset (compiled_data.json)- 08_fluctuation_analysis/ Ion number fluctuation statistics (Fano factor) Note: Final manuscript figure PDFs are intentionally not included in thisarchive (copyright held by the publisher). All figures can be reproduced byrunning 05_analysis_scripts/generate_figures.py and generate_figure5.py onthe included data. Production trajectory files (prod.nc, ~1.5 TB total) are not included due tosize constraints; they can be regenerated from the included input files andtopologies using AMBER24 with pmemd.cuda. License: CC BY 4.0