RNA Hairpin MD Simulation Repository

Computational research repository for RNA hairpin folding dynamics using classical molecular dynamics and weighted ensemble sampling.

Systems: 1hs3 RNA hairpin (DE Shaw and OL3 force fields) and 2KOC UUCG tetraloop variant Methods: AMBER MD, WESTPA weighted ensemble, cpptraj trajectory analysis, barnaba eRMSD Cluster: Notre Dame CRC (SGE scheduler, module load amber/24.0, rna conda environment)

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Directory Structure

md_protocol/       AMBER simulation protocol: tLeap setup, equilibration, production, analysis tools
simulations/       Active simulation systems — force-field setups, equilibration, production runs
westpa/            Weighted ensemble (WESTPA) rare-event sampling configurations
utils/             Miscellaneous repository utilities (archiving, deployment, format conversion)

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Simulation Systems

Three active systems in simulations/:

System	Force Field	Water Model	Notes
1hs3_DEShaw/	DE Shaw RNA	TIP4P-D	System setup only
1hs3_OL3/	Amber f99+bsc0+χOL3	TIP3P	Full min/eq/production
2KOC_OL3_HRM/	Amber f99+bsc0+χOL3	TIP3P	14-residue UUCG tetraloop; folded + unfolded states

All production runs: NVT 300 K, Langevin thermostat (γ = 1.0 ps⁻¹), 2 fs timestep, 50 M steps (100 ns) per block. See simulations/README.md.

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Weighted Ensemble Sampling

Setup	Pcoord	Notes
westpa/Example1D_RMSD/	1D RMSD	Template/reference (incomplete)
westpa/Example2D_RMSDMinDist/	2D: RMSD × MinDist	Active, 280 bins, recursive mapper

See westpa/README.md.

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Running the Analysis Pipeline

cd md_protocol/03_analysis/claude_cpptraj_pipeline

# Edit full_pipeline.py: set TOTAL_NS, topology/trajectory paths, metric config
python full_pipeline.py

# Submit to CRC cluster
qsub submit_pipeline.sh

Outputs per-observable time-series plots, ermsd_metrics.csv (master table with eRMSD, RMSD, RoG, MinDist, LoopRMSD), and all 2D cross-metric plots. See md_protocol/03_analysis/claude_cpptraj_pipeline/README.md.

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Key Dependencies

• Python: numpy, pandas, matplotlib, barnaba, pillow
• AMBER 24.0+: cpptraj, tleap, antechamber, parmchk2
• On cluster: module load amber/24.0 → conda activate rna