Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction

Dataset relative to Molecular dynamics simulation performed for the work "Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction".

The dataset contains data of 42 alchemical simulations and is subdivided in 4 zip files.

Folders are named following the scheme: system_configuration_forcefield.
Zip file C1 contains .mdp files used for all the simulations.

Folders corresponding to simulations performed with the fit5_AC ff contains:
- topology files (topol.top, topol_RNA_chain_A.itp, topol_RNA_chain_B.itp)
- index files needed to reconstruct the demuxed trajectories (replica_index.xvg , replica_index.xvg)
- 16 folders, one for each replica (lam0 ... lam15), containing:
   - final configuration (confout.gro)
   - log file (md.log)

  - input file for md run (md.tpr)
   - energies for the concatenated trajectories recomputed for the realtive replica hamiltonian (ener_trj_conc.edr)

Folders corresponding to simlations performed with fit_A parametrization only contains .edr files corresponding to energies for the concatenated trajectory computed for 14 set of DeQs drawn from  a gaussian distribution, with the relative topologies.

Supplementary materials relative to simlations performed with fit_A parametrizationcan be found in: https://zenodo.org/records/6498021