110 lines
3.0 KiB
Plaintext
110 lines
3.0 KiB
Plaintext
# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11
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# with various Rso setting as well as run of reference system for time comparison (real units)
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# The first run writes restart file that is used by all subsequent runs.
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# Run relres with Rso=6.25
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units real
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atom_style molecular
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boundary p p p
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dielectric 1
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special_bonds lj/coul 0.0 0.0 0.5
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bond_style harmonic
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angle_style harmonic
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dihedral_style fourier
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pair_style lj/relres 5.75 6.25 12.0 14.0
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read_data Data.22DMH.in.real
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pair_coeff 6 6 0.175 3.905 0.0 0.0
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pair_coeff 4 4 0.118 3.905 0.0 0.0
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pair_coeff 2 2 0.118 3.905 1.2218 3.905
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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pair_coeff 3 3 0.118 3.905 0.0 0.0
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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run 1000
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write_restart restart.relres.real
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# Run relres with Rso=7.25
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clear
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read_restart restart.relres.real
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pair_style lj/relres 6.75 7.25 12.0 14.0
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pair_coeff 6 6 0.175 3.905 0.0 0.0
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pair_coeff 4 4 0.118 3.905 0.0 0.0
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pair_coeff 2 2 0.118 3.905 1.2218 3.905
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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pair_coeff 3 3 0.118 3.905 0.0 0.0
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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run 1000
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# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group
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clear
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read_restart restart.relres.real
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pair_style lj/relres 6.75 7.25 12.0 14.0
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pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0
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pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0
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pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0
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pair_coeff 5 5 0.145 3.960 0.0 0.0
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pair_coeff 3 3 0.118 3.905 0.0 0.0
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pair_coeff 1 1 0.05 3.8 2.9128 3.9309
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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run 1000
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# Run reference system with lj/smooth
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clear
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read_restart restart.relres.real
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pair_style lj/smooth 12.0 14.0
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pair_coeff 6 6 0.175 3.905
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pair_coeff 4 4 0.118 3.905
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pair_coeff 2 2 0.118 3.905
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pair_coeff 5 5 0.145 3.960
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pair_coeff 3 3 0.118 3.905
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pair_coeff 1 1 0.05 3.8
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pair_modify shift yes
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neighbor 2.0 bin
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neigh_modify every 2 delay 4 check yes
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timestep 1.0
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thermo 100
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thermo_style custom step temp press pe ke etotal epair emol vol
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fix 2 all nvt temp 290 290 2.0e+02
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run 1000
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