Hello all,
I’ve been struggling to solve a problem that I haven’t yet been successful at it. I want to adjust the pressure of water confined between two walls at 1 bar before experiencing a Couette shear flow. Initially before applying shear flow, the pressure of water is around 150000 bar. I used npt to adjust the pressure which at the end of the MD run fluctuates around 1 bar. The visualization of the trajectory shows the formation of holes in liquid water. I have attached a snapshot of such holes. I don’t know how to set up my simulation to avoid the system from behaving like that. I wonder if anyone can help me about it.
Regards,
Farshad
PS. The input file is as follows:
read_restart restart.equil_nvt_298K.100000
neighbor 3.0 bin
neigh_modify delay 0 every 10 check yes
set potential function and parameters
Create Groups
group hy type 5 # H_water
group ox type 6 # O_water
set group ox charge -0.8476
set group hy charge 0.4238
group water type 5 6 # water
group slab type 1 2 3 4 # slab
pair_style hybrid/overlay rebo lj/cut 7.5 lj/cut/coul/long 8.5
pair_coeff * * rebo CH.airebo C H C H NULL NULL
pair_coeff * * lj/cut 0.0 0.0
pair_coeff * * lj/cut/coul/long 0.0 0.0
pair_coeff 1 6 lj/cut 0.013 2.71
pair_coeff 2 6 lj/cut 0.0036 1.7753
pair_coeff 3 6 lj/cut 0.013 2.71
pair_coeff 4 6 lj/cut 0.0036 1.7753
pair_coeff 6 6 lj/cut/coul/long 0.0067 3.166
bond_style harmonic
bond_coeff 1 7.669 1.0
angle_style harmonic
angle_coeff 1 1.829 109.47
kspace_style pppm 1.0e-5 #final npt relaxation
timestep 0.001
fix freeze slab setforce 0.0 0.0 0.0
compute temp_water water temp
compute press_water all pressure temp_water
thermo 500
thermo_style custom step pe etotal press temp c_press_water c_temp_water
thermo_modify norm no
fix shake_4 all shake 1e-5 20 0 b 1 a 1
fix npt_1 all npt temp 298.0 298.0 0.01 iso 1.0 1.0 1.0
fix_modify npt_1 press press_water temp temp_water
dump dcd_4 all dcd 500 equil_npt_298K.dcd
run 50000
write_restart restart.equil_npt_298K.*
