I simulated a system with silicon dioxide and water, where a cluster of cylindrical water molecules was initially placed on the surface of silicon dioxide. The silicon dioxide was modeled using Emami et al.'s force field (https://pubs.acs.org/doi/10.1021/cm500365c), while water was modeled using the SPC/fw model. When I used the command ‘special_bonds 0 0 1’, the water molecules quickly dispersed and then gradually recondensed. However, when changed to ‘special_bonds 0 0 0’, the water molecules remained clustered. This suggests that the ‘special_bonds’ command altered the interactions between silicon dioxide and water or among the water molecules. This seems anomalous to me because ‘special_bonds’ should only affect interactions between directly or indirectly bonded atoms. Where might my understanding have gone wrong? I have attached my code below and upload the data file.
Q4_1000water.data (4.5 MB)
boundary p p p
units real
atom_style fullpair_style lj/cut/coul/long 12
bond_style harmonic
angle_style harmonic
pair_modify mix arithmeticread_data Q4_1000water.data
group water type 5 6
group sio2 type 1 2 3 4kspace_style pppm 1e-6
special_bonds lj/coul 0 0 1
velocity all create 298.15 85417 dist gaussian
fix 1 all nvt temp 298.15 298.15 $(100*dt)
timestep 1
thermo 1000
dump 1 all custom 1000 Q4_1000water.dump id type x y z vx vy vz
run 3000000
Thanks a lot for any help.
Jianghui