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The observed s-value is consistent with a monomer of the silver nanoparticle, and therefore the molar mass can be constrained using the known molar mass available from the crystal structure.
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The locations of the SMGAs are constrained using the back-propagation method of Kurahashi and Irikura (2010).
Covalent bonds containing hydrogen atoms were constrained using the SHAKE algorithm, and the long-range electrostatic interactions were treated by the Particle Mesh Ewald (PME) method.
All bonds involving hydrogen atoms were constrained using the SHAKE algorithm [42] and the non-bonded cut-off was set to 10.0 Å.
The model was constrained using the present topographic surface, the maximum flooding line of the Holocene transgression, architecture and texture of depositional wedge, the location of coastlines, aeolian dunes and ancient offshore delta-sand.
The differences in these two conditions might explain the differences in peak slips between our models and the USGS solutions (Hayes, 2011), which were constrained using the same software.
The bond lengths were constrained using the SHAKE algorithm [50].
In the simulation, the covalent bonds to hydrogen atoms were constrained using the SHAKE algorithm [40].
The SETTLE algorithm [42] was used to preserve the bond lengths in water molecules, while the lipid bond lengths were constrained using the LINCS algorithm [43].
Neighbor lists were utilized and updated every five steps, and all protein and water bond lengths were constrained using the LINCS and SETTLE algorithm, respectively [27].
During the MD runs, the LINCS algorithm [44] was used in order to constrain the lengths of all bonds; the water molecules were constrained using the SETTLE algorithm [45].
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