All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions

Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript. Scripts which were used to extract hydrogen bond information are available on https://github.com/salvatoredimarco/rna-membrane Systems: 4xN: nucleosides 4xN2: dinucleotides 4xN3: trinucleotides 4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding. 1xGA, 1xGU, 1xGC, 1xCU 1xGGC, 1xGCG 1xquadruplex: G-quadruplex 1xstrand: 19-mer RNA strand 1xhairpin: 16-mer folded hairpin 1x16mer_elong: 16-mer unfolded, restrained 2x16mer_loose1/2: 16-mer unfolded, unrestrained