This repository contains the published data, Jupyter Notebooks and input data to generate the plots found in "Benchmarking RNA all-atom force fields using a set of diverse hairpin motifs" by Dimitrios Stamatis, Chandra S. Verma, and Jonathan W. Essex.
Working paper version: https://doi.org/10.26434/chemrxiv-2023-0j7p4
Github repo: https://github.com/essex-lab/2024_Stamatis-RNA_FF_benchmark
Full dataset: https://doi.org/10.5281/zenodo.10715633
gmx_FFs/ contains the Gromacs-compatible force field libraries used in this study.
REST2_dynamics/ contains simulation input files (including .trp files for each replica), output trajectories, and reference structures used during analysis (base-replica trajectories are omitted; full dataset can be found on Zenodo).
Analysis/notebooks/ contains Jupyter notebooks to calculate eRMSDs, G-vectors, η/θ pseudotorsions, and specific internucleotide distances and torsions, as well as to perform cluster-based anaylsis.
Analysis/{UUCG,AUCG,CUUGU,GUAAU}/Gvec_conformations contain input to reproduce published analysis data (pre-calculated G-vectors are omitted; full dataset can be found on Zenodo).
Python packages:
- Numpy
- Pandas
- Matplotlib
- Scikit-learn
- MDTraj
Other:
- Gromacs (2018.8 or later)
- ParmEd
- baRNAba