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Protocol for classical molecular dynamics simulations of nano-junctions in solution
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Image of FIG. 1.
FIG. 1.

Semi-infinite Au slabs (top and bottom) partially surrounded by water.

Image of FIG. 2.
FIG. 2.

(a) Input configuration. (b), (c) Result after heating using UFF and HVFN parameters, respectively.

Image of FIG. 3.
FIG. 3.

Behavior of a water droplet on an Au(111) surface, calculated by using either the HVFN (top) and UFF (bottom) parameters.

Image of FIG. 4.
FIG. 4.

Comparison of the O-O (TIP3P) Lennard-Jones interaction potential with the Au-O potential that results from combination rules between van der Waals parameters for O and HVFN (top) and UFF (bottom) parameters for Au.

Image of FIG. 5.
FIG. 5.

Fluctuation of the number of water molecules in the selected volume of interest for the last 5 ns of the trajectory.

Image of FIG. 6.
FIG. 6.

Variation of the number N along the x-axis, based on bins of equal size (a-j).

Image of FIG. 7.
FIG. 7.

Linear fits of the z and Au-Au distances against N.

Image of FIG. 8.
FIG. 8.

Water density profiles along x (top) and along z (bottom) with and without the CNT.

Image of FIG. 9.
FIG. 9.

Order parameter as a function of the distance from the center of the nanotube (r) for different spatial regions in the presence (S8) and absence (S6) of a nanotube.


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Table I.

Sizes and particle numbers of the model systems.

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Table II.

Number N and standard deviation of water molecules averaged over various time blocks and for different selection criteria.

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Table III.

Estimates of N and density for the different types of simulation and input parameters.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Protocol for classical molecular dynamics simulations of nano-junctions in solution