The interaction between the surface and the difenoconazole molecule was investigated in the vacuum using a large number of randomized Monte Carlo steps (975,956,401 configurations). The MD calculations continued to use the lowest energy pose provided by MC. Prior to the MD stage, the geometry of the simulation boxes was optimized (tolerance for energy convergence of 1 × 10−5 kcal/mol; atom-based summation method used for both electrostatic and van der Waals interactions with a cutoff distance of 15.5, a spline width of 1, and a 0.5 buffer) using the Forcite module included in the Biovia software. MD was performed at 25 °C using the constant volume/constant temperature (NVT) canonical ensemble with a simulation time of 500 ps (1 fs time step) [50,51,52,53]. The Berendsen thermostat maintained the T control. Calculations for MC and MD were performed using the Condensed Phase Optimized Molecular Potential II (COMPASSII) forcefield [54,55,56,57,58,59].

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