Single-Chain Molecular Dynamics Trajectories and Analysis Code for Human Nuclear Pore Inner-Ring FG-Repeat Sequences

Each sequence was simulated as an isolated chain using two all-atom explicit-solvent force-field/water-model combinations, AMBER99SB/OPC and CHARMM36m/TIP3P, resulting in eight molecular dynamics systems.For each system, the final 500 ns analyzed in the associated study is provided as a matching structure and analysis-ready protein-only trajectory pair in GRO/XTC format, comprising 25,001 frames at 20 ps intervals.

The deposit also contains simulation parameter and topology-related files, trajectory preprocessing commands, analysis code (version 4.1.0-public), CALVADOS and Mpipi FINCHES matrices, machine-readable results, validation reports, software-environment records, and a SHA-256 checksum manifest.The analyses include global conformational dimensions, side-chain-heavy-atom binary contacts, sequence-separation-normalized C-alpha distances, sliding-window regional evidence, cross-model residue-pair and chemical-class comparisons, chemical-class observed/expected enrichment, temporal-block support, and parameter-sensitivity analyses.