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