Paper Citing NAMD - Abstract
Connolly, M. J.; Roth, M. W.; Gray, Paul A.; Wexler, Carlos
Explicit hydrogen molecular dynamics simulations of hexane deposited onto graphite at various coverages
LANGMUIR, 24:3228-3234, APR 1 2008
We present results of molecular dynamics (MD) computer simulations of hexane (C6H14) adlayers physisorbed onto a graphite substrate for coverages in the range 0.5 <= rho <= 1 monolayers. The hexane molecules are simulated with explicit hydrogens, and the graphite substrate is modeled as an all-atom structure having six graphene layers. At coverages above about rho congruent to 0.9 the low-temperature herringbone solid loses its orientational order at T-1 = 140 +/- 3 K. At rho = 0.878, the system presents vacancy patches and T-1 decreases to ca. 100 K. As coverage decreases further, the vacancy patches become larger and by rho = 0.614 the solid is a connected network of randomly oriented islands and there is no global herringbone order-disorder transition. In all cases we observe a weak nematic mespohase. The melting temperature for our explicit-hydrogen model is T-2 = 160 +/- 3 K and falls to ca. 145 K by rho = 0.614 (somewhat lower than seen in experiment). The dynamics seen in the fully atomistic model agree well with experiment, as the molecules remain overall flat on the substrate in the solid phase and do not show anomalous tilting behavior at any phase transition observed in earlier simulations in the unified atom (UA) approximation. Energetics and structural parameters also are more reasonable and, collectively, the results from the simulations in this work demonstrate that the explicit-hydrogen model of hexane is substantially more realistic than the UA approximation.
