| # 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. |
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