SRP-sliding-dynamics

Input files for the molecular dynamics simulations of cyclodextrin (CD) rings threaded on poly(ethylene glycol) (PEG) — the single-ring polyrotaxanes and dimers that are the molecular building blocks of slide-ring polymers (SRPs) — used to study ring sliding/diffusivity and dimer binding free energies under applied tension.

These are inputs only (topologies, force-field parameters, run parameters, starting structures, and PLUMED inputs). Trajectories and other large outputs are not included.

Layout

forcefield/                shared force field (identical across all systems)
  gaff2.itp  tip3p.itp  PEG_30_c_GMX.itp
  MOL_aCD-OH.itp  MOL_aCD-OC.itp  MOL_gCD-OH.itp  MOL_gCD-OC.itp   (per CD type)
mdp/                       shared GROMACS run parameters
  0_minim.mdp  1_equil.mdp  2_NPT.mdp  3_NVT.mdp
unbiased/<CD>/<chem>/<state>/<length>/    diffusivity (unbiased) runs
biased/<CD>/<chem>/<config>/<length>/     OPES binding-free-energy runs

Each leaf folder contains its unique inputs (topol.top, starting .gro, and plumed.dat for biased runs) plus a run.sh template. The topol.top #include lines point to the shared forcefield/ directory.

System key

• CD: aCDs = α-CD, gCDs = γ-CD (+1 PEG), gCDd = γ-CD (+2 PEG, double-threaded)
• chem: OH = native CD, OC = permethylated (PM-) CD
• state (unbiased): 0 = single ring (monomer); 1/2/3 = two-ring dimer (FT/TT/FF)
• config (biased): 1/2/3 = dimer orientation FT/TT/FF
• length lN: the extent of the simulation box along the chain (z) axis in nm, which sets the extension — and hence the applied tension — on the PEG chain. l8 = 8 nm, l9 = 9 nm, …, l14 = 14 nm. The labels l16–l19 denote additional intermediate box lengths (not 16–19 nm) used to add extra tension points. aCDs_trans/ = PEG restrained to the all-trans backbone conformation.

Running a simulation

From any leaf folder (mdps are referenced from the repo-root mdp/):

cd unbiased/aCDs/OH/0/l8
bash run.sh          # em -> equil -> NPT -> NVT

cd biased/aCDs/OH/3/l11
bash run.sh          # OPES production with plumed.dat

run.sh is a template — adjust GROMACS/cluster settings for your environment. Requires GROMACS (patched with PLUMED for the biased runs).

Starting structures. Unbiased runs start from the solvated structure system-water.gro, which is energy-minimized in the first step of run.sh. Biased runs start from the provided pre-minimized structure 0_em.gro.

Citation

If you use these inputs, please cite the accompanying paper. A preprint is available on ChemRxiv: https://chemrxiv.org/doi/full/10.26434/chemrxiv.15005291/v1 (journal reference to be updated upon publication).

Trajectory data are not included in this repository and are available from the corresponding author on request.