units real atom_style full boundary p p p dielectric 1 special_bonds lj/coul 0.0 0.0 1.0 # Charmm 1-4 interaction coeff should be zero in data file. #pair_style lj/charmm/coul/long 10.0 12.0 pair_style lj/charmm/coul/charmm 10.0 12.0 bond_style harmonic angle_style cosine/squared # without CO2 (linear geometry) dihedral_style charmm improper_style umbrella #kspace_style pppm 0.0001 read_data gcmc.data pair_modify mix arithmetic neighbor 1.4 bin neigh_modify every 1 delay 0 check yes thermo_style multi thermo 10 variable input index in.gcmc variable sname index gcmc molecule 9999 co2.txt group co2 molecule 9999 compute_modify thermo_temp dynamic yes #print . #print ========================================== #print "500 steps CG Minimization" #print ========================================== #print . # #dump 1 all atom 25 ${sname}.min.lammpstrj #dump_modify 1 image yes scale no #min_style sd #minimize 1.0e-4 1.0e-4 500 5000 #min_style cg #minimize 1.0e-4 1.0e-4 500 5000 ##now minimize the entire system #minimize 1.0e-4 1.0e-4 500 5000 #undump 1 print . print ===================================== print "NVT dynamics to heat system" print ===================================== print . reset_timestep 0 timestep 1.0 velocity all create 0.0 12345678 dist uniform dump 1 all atom 1 ${sname}.heat.lammpstrj dump_modify 1 image yes scale no sort id fix 2 all nvt temp 298.0 298.0 100.0 fix 3 co2 gcmc 1 10 10 10 123456 298.0 -0.5 0.1 mol 9999 maxangle 180 pressure 0.15 run 2 #run 1000000 unfix 3 unfix 2 undump 1 #print . #print ================================================ #print "NPT dynamics with an anisotropic pressure of 1atm." #print ================================================ #print . # #reset_timestep 0 #dump 1 all atom 100 ${sname}.npt.lammpstrj #dump_modify 1 image yes scale no #fix 2 all npt temp 298.0 298.0 100.0 aniso 1.0 1.0 2000.0 #run 200000 #unfix 2 #undump 1 #print . #print ========================================== #print "NVE dynamics" #print ========================================== #print . # #dump 1 all atom 1 ${sname}.lammpstrj #dump_modify 1 image yes scale no #thermo 10 #fix 2 all nve #velocity all create 298.0 4928459 rot yes dist gaussian #run 2000 #unfix 2 #undump 1