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Fig. 16 Meso-dodecamer (
left
and
center
) and its atomistic reconstructured model (
right
)
chosen to be neutral, which led to an overall increase in the times spanned during
simulations.
A 1.4-
˚
crystal structure of the B-DNA dodecamer (355D) was solvated in a
TIP3 water box and neutralized. This fully atomistic structure was simulated using
the usual procedure for 2 ns of NPT dynamics, with snapshots of the last 500 ps
(every 5 ps) saved for thermodynamic and structural analysis. The average MD
structure was calculated as before and the ions were removed. It was then converted
into its mesoscale description, with the waters modeled as inflated van der Waals
spheres. This water model is the same as the M3B model from our previous work in
Molinero et al. [
124
], and was parameterized to reproduce the density, diffusivity,
and cohesive energy of experimental bulk water. The mesoscale dodecamer is then
simulated for 2
10
6
steps, representing 2
m
s of total simulation time. Snapshots of
the system during the last 50 ns of simulation were saved and used for thermody-
namic and structural analysis. The average MD structure during the last 50 ns was
calculated and the atomistic level description reconstructed from this average
structure. This reconstructed atomistic structure was then minimized and simulated
for 1,000 steps of NPT dynamics (Fig.
16
).
Comparison of Meso-Scale and Atomistic Dodecamer Simulations
Timing tests indicate that the atomistic level simulation took twice as long to
complete 2 ns than the meso-scale did to complete 2
m
s (150 vs 69 CPU hours).
This is remarkable, and represents a 2,000
speedup for the meso-scale model.
This opens the door for studying DNA system in the micro-second timescale.
As a measure of the similarities between the meso, atomistic, and crystal
structures, we calculate the CRMS. We find that the simulation structures are
quite different from the crystal structure (5.5
˚
and 3.2
˚
for meso and atomistic,
respectively), as well as from each other (4.7
˚
difference between the two). This is
further illustrated in Fig.
17
, where the average MD structures of both the meso-
scale and the atomistic structures are compared. A smooth backbone profile can be
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