This repository contains sample notebooks and input files to two manuscripts:
- Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine, also available as arXiv:2203.14886. Trajectory files, as well as all input files used for molecular dynamics simulations, can be found on Zenodo.
- [Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction] (https://pubs.acs.org/doi/10.1021/acs.jpcb.4c03397), also available as arXiv:2404.14821. Trajectory files, as well as all input files used for molecular dynamics simulations, can be found on Zenodo. PLUMED input files are also shared on the PLUMED-NEST
