protocol/PROTOCOL.md

RNAmd v1 Simulation Protocol

RNAmd v1 uses a uniform GROMACS OL3/TIP3P workflow for the public trajectory layer. The compact public release contains processed RNA-only trajectories, paired RNA-only structures, QC summaries and dynamic labels. Raw full-system TRR trajectories remain in the server archive because they are too large for the compact public v1 mirror.

Software and model

• MD engine: GROMACS 2024.5-conda_forge, mixed precision, MPI/OpenMP build with CUDA support on the production cluster.
• Force field: AMBER RNA OL3/OL15 workflow through pdb2gmx -ff amber14sb_OL15 -water tip3p -ignh.
• Water and ions: TIP3P-compatible spc216.gro water box, neutralized with K+ and Cl- ions using genion.
• Box and PBC: dodecahedral box, 1.2 nm solute-to-box padding and pbc = xyz.
• Electrostatics/cutoffs: Verlet cutoff scheme, PME electrostatics, 1.0 nm Coulomb and van der Waals cutoffs, fourth-order PME and 0.12 nm Fourier spacing.
• Constraints: 2 fs MD time step with hydrogen-bond constraints and LINCS (lincs_iter = 1, lincs_order = 4).

MD stages

Stage	Length / stopping rule	Main parameters
Ion placement	GROMACS preprocessing	Steepest-descent parameter file with nsteps = 0; neutralizing ions before minimization.
Energy minimization	Up to 50,000 steps	Steepest descent with positional restraints, emtol = 500.0, emstep = 0.01.
NVT equilibration	100 ps	Positional restraints, V-rescale thermostat at 300 K, tau-t = 0.1, generated velocities at 300 K.
NPT equilibration	1 ns	Positional restraints, V-rescale 300 K and isotropic C-rescale pressure coupling at 1 bar with tau-p = 2.0.
Sentinel production	1 ns	Unrestrained MD from NPT output; full production was retained only after status and performance checks.
Main production	99 ns after sentinel, 100 ns total	Unrestrained MD with V-rescale 300 K, C-rescale 1 bar, PME, PBC, dispersion correction and coordinate output every 10 ps in the raw trajectory.

Public trajectory processing

Raw full-system outputs are converted to RNA-only public products with gmx trjconv. The default public trajectory is a PBC-processed RNA-only XTC at 100 ps stride, paired with RNA-only GRO and PDB files. Conversion uses centering, molecular PBC handling, compact unit-cell output and rotational/translational fitting.

QC and release inclusion

RNAmd v1 includes entries with completed 100 ns standardized simulations and public structure/metadata records. Partial runs, failed runtime checks and incomplete status records were excluded from the 882 released samples. Residue dynamic labels are reported for 880 samples and contact labels for 877 samples; very short RNAs or structures with too few eligible phosphate atoms/nonlocal contacts remain in the manifest but have no corresponding label rows.

File integrity is verified with package-level SHA-256 checksums and inventory tables. Website QC tables expose measured RMSD, radius-of-gyration, flexibility and contact summaries rather than imposing an additional hard pass/fail filter on completed release entries.