taseef/BENDER-MPIPI

BENDER-MPIPI

Companion dataset to BENDER. Contains coarse-grained molecular dynamics trajectory data from MPIPI (Multi-scale Platform for Intrinsically disordered Protein Interactions) simulations of intrinsically disordered proteins (IDPs).

Contents

Trajectories are organized by taxonomic kingdom. Each zip file contains subdirectories named by UniProt ID, with the following files per protein:

• —traj.xtc — trajectory file
• —log.lammps — LAMMPS simulation log
• —Rg.out — radius of gyration output
• —run.in — LAMMPS input script
• —run.sh — run script
• —seq.dat — sequence data

Sequences per Kingdom

Simulation Details

All simulations use the Mpipi-GG (v23-r1) coarse-grained force field (Lotthammer et al., *Nat Methods* 2024), run with LAMMPS. The protocol mirrors the CALVADOS IDRome adaptive scheme:

Force Field & Representation

• —One-bead-per-residue coarse-grained model (C-alpha representation)
• —Bond potential: Harmonic, k = 9.6 kcal/mol/A^2, r0 = 3.81 A
• —Non-bonded interactions: Wang-Frenkel (WF) potential with cutoff 25.0 A
• —Electrostatics: Coulomb/Debye screening at 150 mM implicit salt (kappa = 0.126 A^-1)
• —Charged residues: K, R (+0.75e); D, E (-0.75e)
• —Dielectric constant: 80.0

Simulation Protocol

• —Integrator: NVE + Langevin thermostat (equivalent to NVT)
• —Temperature: 300 K, damping = 5000 fs
• —Timestep: 20 fs
• —Boundary conditions: Periodic (PBC)
• —Box size: 500 A for sequences <= 300 residues; (N/5 + 20) x 10 A for longer sequences
• —Initial configuration: Self-avoiding random walk, followed by energy minimization

Adaptive Simulation Length

• —Sequences <= 150 residues: 200 ns total
• —Sequences > 150 residues: 200 x (N/150)^2 ns (quadratic scaling)
• —Equilibration: First 50% of trajectory discarded
• —Production frames: 10,000 (<=300 ns), 15,000 (<=600 ns), or 20,000 (>600 ns)

Output

• —traj.xtc — XTC trajectory (production frames only, post-equilibration)
• —Rg.out — Radius of gyration time series
• —log.lammps — Full simulation log with thermodynamic properties
• —seq.dat — LAMMPS data file with sequence, topology, and initial coordinates
• —run.in — Complete LAMMPS input script (fully reproducible)

Citation

@misc{sabian98_2026,
	author       = { Taseef Rahman },
	title        = { BENDER-MPIPI (Revision 57dd8bf) },
	year         = 2026,
	url          = { https://huggingface.co/datasets/taseef/BENDER-MPIPI },
	doi          = { 10.57967/hf/10438 },
	publisher    = { Hugging Face }
}