The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations

We investigated to characterize the dynamics of protein-RNA complexes and their interfaces at molecular level by performing a more systematic analysis. To get insights on the dynamics of protein-RNA complexes, all-atom MD simulations were generated for the manuscript "The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations". Nine protein-RNA complexes are studied in this work: 1ASY (an aspartyl-tRNA synthase/tRNA), 1JBS (a ribotoxin restrictocin/SRD RNA), 1MMS (a ribosomal protein L11/23S), 1OOA (a nuclear factor NF-kappaB p105 subunit/RNA aptamer), 1RKJ (a nucleolin/pre-rRNA), 2R8S (a FAB/P4-P6 RNA ribozyme domain), 2VPL (a 50S ribosomal protein/mRNA), 2ZM5 (a tRNA delta(2)-isopentenylpyrophosphate transferase/tRNA), 3IEV (a GTP-binding protein era/3' end of 16S rRNA). 
Each folder for a complex is organised as followed:

in complex there are the dry MD simulations for the complex protein-RNA with the starting structure
in protein there are the dry MD simulations for the unbound protein with the starting structure
in rna there are the dry MD simulations for the unbound RNA with the starting structure
In each folder, all the trajectory files are named : md_(times of simulations).xtc and the starting structure called : start.gro.