NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference

This repository contains molecular dynamics (MD) trajectories for RNA internal loop sequences involving the GAGU motif. Simulations were conducted to complement NMR findings and explore how flanking base pairs and ionic conditions influence structural dynamics and conformational preferences. --- ## 🗃️ File formatFiles are stacked pdb format, created using Amber cpptraj. ## 🗃️ File Naming Convention Trajectory files follow the format: traj.pdb.[salt].[flanking_sequence].start[conformation]-rep-[replicate_id].tar.gz- `salt`: Salt condition (`100mM` or `1M`, for 0.1 M or 1 M K⁺, respectively)- `flanking_sequence`: The sequence flanking the GAGU loop (e.g., `CG`, `AU`, `UA`, `GC`)- `start[conformation]`: Starting conformation (`I`, `III`)- `rep-[id]`: Replicate number (1,2,3,4) **Example:** "traj.pdb.100mMsalt.CgaguG.startIII-rep-1.tar.gz" representsrepresents replicate 1 of a simulation with:- CG flanking sequence- Starting in conformation III- 0.1 M (100 mM) K⁺ concentration ## ⚙️ Simulation Details - **Force Field**: AMBER.RNA.OL3- **Ionic Conditions**: 0.1 M or 1 M K⁺- **Total Simulation Time**: 1 microsecond per replicate- **Frame Resolution**: Snapshots recorded every 100 ps- **Water and Ions**: Solvent-stripped trajectories