Molecular dynamics simulations of Me₄Bipip binding to sulfated prism[6]arene (Pr[6]AS): simulation inputs, analysis code, and cached results

Simulation inputs, analysis code, and cached results supporting the computational section of "Sulfated Prism[6]arene Binds One Guest Internally and One Guest Externally". The molecular dynamics show how the dicationic guest Me₄Bipip binds the anionic host Pr[6]AS: one guest threads the cavity and a second binds externally at the sulfated portal, giving a 1:2 complex with one internal and one external guest.Systems. Four setups, nine production trajectories, and one minimization-only control: uncomplexed Pr[6]AS (52 ns); Pr[6]AS·Me₄Bipip 1:1 (500 ns × 2 replicates); Pr[6]AS·(Me₄Bipip)₂ 1:2 started from a one-in/one-out geometry (500 ns × 3); the same 1:2 stoichiometry started with both guests unbound in solution (500 ns × 3), which assembles spontaneously to the same topology; and a control with both guests force-docked into the cavity, for which no stable force-field minimum exists. Methods. OpenFF Sage 2.3.0 with NAGL machine-learned AM1-BCC charges for the host and AM1-BCC charges for the guest, TIP3P water, Joung–Cheatham ions, PME with a 0.9 nm cutoff, unbiased NPT production in OpenMM at 300 K with a 2 fs timestep. Analysis with MDTraj. Structure preparation and charge assignment; system build, equilibration, and production scripts including the two-guests-in-cavity control; 39 analysis scripts covering binding mode, host shape, hydration, counterion coordination, and simulation quality control; per-system OpenMM inputs (system.xml, solvated and equilibrated coordinates, restart checkpoints, and every stage log) for all ten systems; cached analysis results as .npz archives, representative-frame PDBs, and water-density grids; and the Supporting Information text and figures. README.md explains the directory layout and how to reproduce the results, and COMMANDS.md gives the invocation of every analysis script.