# Mol1-graphene-water #################### Initialization #################### boundary p p p units real atom_style full bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 pair_style soft 9.5 pair_style lj/class2/coul/long 9.5 pair_modify tail yes table 12 #################### Atom Definition #################### read_data Molecule.data group all type 1 2 3 4 5 6 7 8 9 10 11 group Mol type 4 5 6 7 8 9 10 11 group P_G type 1 4 5 6 7 8 9 10 11 group G type 1 group water type 2 3 #################### Settings #################### kspace_style ewald 1e-4 special_bonds dreiding neighbor 1 bin neigh_modify delay 0 every 1 check yes page 1000000 comm_modify mode single cutoff 9.5 vel no #################### Minimization #################### thermo 100 thermo_style custom step temp press vol density etotal ke pe time minimize 1.0e-06 1.0e-06 100000 100000 ### Preliminary velocities ### velocity all create 290 53673542 units box #################### Run #################### reset_timestep 0 fix shsh water shake 0.000001 1000 0 t 2 3 b 2 a 2 fix 1 all npt temp 290 290 100 iso 1 1 1000 dump 1 all xyz 500 dump-total.xyz dump 11 all custom 500 dump-total.lammpstrj id mol type element mass q x y z xs ys zs #+++ Interaction Energy and Force +++# #compute Interaction01 Mol group/group G kspace yes #fix Interaction01 all ave/time 1 500 500 c_Interaction01 c_Interaction01[1] c_Interaction01[2] c_Interaction01[3] file tmp.interact01 #+++ The Potential of Mean Force +++# fix PMF01 G smd cvel 20 0.0001 couple Mol auto auto auto 0 #fix PMF01 G smd cfor 5 couple Mol auto auto auto 0 fix PMF011 P_G ave/time 1 500 500 f_PMF01[1] f_PMF01[2] f_PMF01[3] f_PMF01[4] f_PMF01[5] f_PMF01[6] f_PMF01[7] file tmp.pmf01 thermo 500 thermo_style custom step temp press vol density etotal ke pe time thermo_modify lost warn flush yes timestep 1 restart 5000 restart.* run 10000 unfix 1 write_data final.data write_restart final.restart