Simulation details Sample Clauses

Simulation details. All MD simulations were performed using the GROMACS 5.0.7 software (Xxxxxxx et al., 2015; Pall et al., 2015; Pronk et al., 2013; Xxxx et al., 2008). The simulations were performed in orthorhombic boxes, with periodic boundary conditions imposed in all directions at ambient conditions of temperature (298.15 K) and pressure (1 bar). These conditions are not only relevant to the ones encountered at earth’s surface but also correspond to the CLAYFF force field parameterization. Prior to production runs and in order to eliminate any close contacts between atoms, all systems were subjected to steepest descent energy minimization for 20,000 steps. Then, short equilibration simulations in the canonical (NVT) and isobaric-isothermal (NpT) ensembles were performed. Specifically, all systems were gradually heated to the target temperatures for 100 ps in the NVT ensemble using the Berendsen thermostat (Berendsen et al., 1984), with the coupling constant set to 1 ps. The LINCS algorithm (Xxxx et al., 1997) restrained all bonds involving hydrogen atoms. The integration step of all simulations was set to 2 fs. A simple cut-off scheme for the Xxxxxxx-Xxxxx (LJ) interactions can have minor impact on the molecular arrangement, but can significantly influence simulations of inhomogeneous systems, leading to incorrect estimation of interfacial properties (Xxxx et al., 2007). Therefore, we applied the Particle Mesh Xxxxx (PME) method (Xxxxxx et al., 1993; Xxxxxxx-Xxxxxx et al., 2013) for the long-range LJ interactions as well as for electrostatic interactions (Xxxxxx et al., 1993) with a cut-off at 1.2 nm for the short-range interactions. The Lorentz–Xxxxxxxxx combining rules (Xxxxx and Tildesley, 1987) were used for the cross-interaction LJ parameters. All systems were initially equilibrated for a period of 1 ns in the NpT ensemble, at constant pressure of 1 bar using a Berendsen barostat (Berendsen et al., 1984), with the coupling constant set to 1 ps. Pressure coupling was isotropic in the x and y direction, but semi- isotropic in the z direction, which is perpendicular to the fluid-kaolinite interface. All systems were further equilibrated for 4 ns using the Nosé–Xxxxxx thermostat (Hoower, 1985), while isotropic pressure was maintained using a Xxxxxxxxxx–Rahman (1981) barostat, with a coupling constant set to 5 ps. During this 5 ns period, the density of the liquid phase converged to a mean value, along with the energy of the system. Finally, production runs of 100 ns were...
Sample 1

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