Skip to main content
. 2012 Jul 2;7(7):e40223. doi: 10.1371/journal.pone.0040223

Figure 6. MD simulations of the RAL-LTR34 and RAL-LTR32 complex systems (PFV oligonucleotides), using GROMACS with the AMBER force field.

Figure 6

(A) Time evolution of RMSD (root mean square deviation) values based on all the heavy atoms for the two LTR34 trajectories (black: LTR34-1 and blue: LTR34-2). RMSD calculations for a single trajectory were also performed using the sugar C4′ atoms (green: LTR34-1) and repeated for LTR34 devoid of 3′-AT (purple). (B) Time evolution of RMSD values of LTR32 for two trajectories (black: LTR32-1 and blue: LTR32-2). (C) RMSF (root mean square fluctuation) variations of sugar C4′ atoms for LTR34 and (D) RMSF variations of sugar C4′ atoms for LTR32.