Water-graphene-water system

Hello everyone,

I have built a water-graphene (4 layers) -water system in Material studio using cvff potential. Then I converted the file in lammps data file using msi2lmp command. Before running any kind of minimization or simulation, I checked the data file’s bond, angle, dihedral and improper parameters along with the cvff file’s parameters, and they were okay. Then I minimized the system with NVE+langevin for 200 ps with 1 fm timestep. The temperature was consistent and hovering around 300-310 K. Although the pressure was high around -90000 atm but it was consistent. But when I ran the NPT with the LAMMPS data file, LAMMPS was saying “triclinic box skew is too large”. I checked the data file to see that the tilt factor in xy is -12.3 which is exactly half the box length. So, it should be between the postive and negative bound of the dimensions of the box. Anyhow, I changed to -5 and -10 and still showed same message. Running NVT also showed same message. Here’s my data file and input file:

DATA FILE:

3449 atoms
2966 bonds
3283 angles
4800 dihedrals
800 impropers
3 atom types
2 bond types
2 angle types
1 dihedral types
1 improper types
-6.281844 18.318156 xlo xhi
0.001894 21.306119 ylo yhi
-0.031351 63.568647 zlo zhi
#-12.300000 0.000000 0.000000 xy xz yz
-5.0000 0.000 0.000000 xy xz yz

PairIJ Coeffs # lj/cut/coul/long

1 1 0.148 3.61705 9.8
1 2 0.151663 3.39128 9.8
1 3 0 1.80852 9.8
2 2 0.155416 3.16552 9.8
2 3 0 1.58276 9.8
3 3 0 0 9.8

Bond Coeffs # harmonic

1 480 1.34
2 540.634 0.96

Angle Coeffs # harmonic

1 90 120
2 50 104.5

Dihedral Coeffs # harmonic

1 12 -1 2

Improper Coeffs # cvff

1 0.37 -1 2

Masses

1 12.011200 # 1
2 15.999400 # 2
3 1.007970 # 3

INPUT FILE:

# water-graphene-water

echo screen
log debug_wgwnpt.log
newton on

units real
atom_style full

bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff

pair_style lj/cut/coul/long 9.8
kspace_style ewald 1.0e-6

neighbor 5.0 bin

#neigh_modify delay 0 every 1 one 10000 check yes
neigh_modify delay 0 every 1 check yes

boundary p p p

read_data data.wgw_nveinterwrap
pair_modify mix arithmetic tail yes

group graphene type 1
group water type 2 3
group oxygen type 2
group hydrogen type 3

#comm_style brick
#comm_modify mode single cutoff 5.0 group all vel yes

set group oxygen charge -0.8476
set group hydrogen charge 0.4238

compute tmpall all temp
compute water_temp water temp
compute graphene_temp graphene temp
compute water_comtemp water temp/com

velocity water create 298.0 12345 temp water_temp
velocity graphene create 298.0 12345 temp graphene_temp

fix 6 water shake 1.0e-4 20 0 b 2 a 2 # N = 0 means shake stats will not be printed in log file

fix 4 all npt temp 298.0 298.0 5.0 iso 1.01325 1.01325 100.0 # Pressure unit in (atm)

timestep 1
thermo 50
#thermo_style one
thermo_style custom step temp pe etotal press vol density
thermo_modify lost error flush yes

dump 1 all xyz 1 graphene1.xyz
dump_modify 1 element C H O

run 5000
write_data data.wgwfinal pair ij