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".<br> <br> 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<br> <br> Folders are named following the scheme: system_configuration_forcefield, or 1M_system_configuration_forcefield for simulation performed at 1 M salt concentrations<br> <br> Each folder contains:<br> - topology files (topol.top, topol_RNA_chain_A.itp, topol_RNA_chain_B.itp)<br> - .mdp files for each replica<br> - index files needed to reconstruct the demuxed trajectories (replica_index.xvg , replica_index.xvg)<br> - 20 .edr files corresponding to energies for the concatenated trajectory computed for 20 set of DeQs drawn from a gaussian distribution<br> - 16 folders, one for each replica (lam0 ... lam15), containing:<br> - final configuration (confout.gro)<br> - log file (md.log)<br> - dhdl.xvg files needed for computing Free Energies via "gmx bar" command<br> - energies relative to the single replica (ener.edr)<br> - energies for the concatenated trajectories recomputed for the realtive replica hamiltonian (ener_trj_conc.edr).