RNADynBench
A standardized all-atom RNA molecular dynamics benchmark.
Each trajectory spans 100 ns with 1,001 frames at 100-ps intervals; standard evaluation uses 101 frames at 1-ns intervals. File formats & units →
Simulated in explicit water and ions; released coordinates contain RNA only. Equilibration is excluded.
A traceable data foundation.
01 / Curate
Experimental RNA structures from RNA-Solo, with molecular context checked against original PDB/mmCIF records.
02 / Simulate
All-atom MD with Amber RNA OL3 and OPC water, at 300 K, 1 bar and 150 mM NaCl.
03 / Validate
Production completion, coordinate continuity, topology and multi-chain behavior checks, with retained diagnostic records.
Two benchmark tasks.
Task 01
Trajectory generation
Start from an initial conformer and generate 101 frames over 100 ns.
Protocol & results →Task 02
Single-conformer prediction
Predict MD-derived residue covariance, RMSF and normalized motion coupling.
Protocol & results →Paper
Citation