Molecular simulations matching denaturation experiments for N6-methyladenosine

Dataset relative to Molecular dynamics simulation performed for the work "Molecular simulations matching denaturation experiments for N6-methyladenosine".

The dataset contains data of 73 alchemical simulations and is subdivided in 10 zip files, one for each of the systems considered in this work

Folders are named following the scheme: system_configuration_forcefield, or 1M_system_configuration_forcefield for simulation performed at 1 M salt concentrations

Each folder contains:
- topology files (topol.top, topol_RNA_chain_A.itp, topol_RNA_chain_B.itp)
- .mdp files for each replica
- index files needed to reconstruct the demuxed trajectories (replica_index.xvg , replica_index.xvg)
- 20 .edr files corresponding to energies for the concatenated trajectory computed for 20 set of DeQs drawn from  a gaussian distribution
- 16 folders, one for each replica (lam0 ... lam15), containing:
   - final configuration (confout.gro)
   - log file (md.log)
   - dhdl.xvg files needed for computing Free Energies via "gmx bar" command
   - energies relative to the single replica (ener.edr)
   - energies for the concatenated trajectories recomputed for the realtive replica hamiltonian (ener_trj_conc.edr).