Graphene/Water Equilibration

Hello everyone,
I am building a model for graphene/water system. I used VMD’s nanobuilder to create the graphene system (540 atoms), and topptools to create water box (360 molecules). I merged the simulation boxes of graphene and water using awk and made LAMMPS data file. I have attached the image for initial geometry.

I am trying to run an equibration with minimize command. The temperatures kept increasing whatever timestep I use. I used 1, 0.1, 0.01, and 0.001 timesteps. For the 1-46 runs, temperature is 0 and after that temperatures kept increasing. I used high amount of damping. I am using NVT with shake command. It showed me the same results when I used NVE. Here is my input file:

water with graphene

echo screen
log debug.log

units real
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
#improper_style cvff

pair_style lj/cut/coul/long 8
kspace_style ewald 1.0e-6

neighbor 2.0 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.mergenewtemp
pair_modify mix arithmetic tail yes

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

set group oxygen charge -0.82
set group hydrogen charge 0.41

#pair_coeff 3 3 0.4396 3.851
pair_coeff 3 3 0.12 3.2963
pair_coeff 2 2 0.15535 3.166
#pair_coeff 2 3 0.392 3.19
pair_coeff 1 1 0.0 0.0
pair_coeff 1 2 0.0 0.0
#pair_coeff 1 3 0.129 2.801
pair_coeff 1 3 0.0 0.0

#bond_coeff 2 702.505 1.472
bond_coeff 2 469 1.4
#bond_coeff 1 1000.00 1.000
bond_coeff 1 554.135 1.000
#angle_coeff 2 80 115
angle_coeff 2 85 120
#angle_coeff 1 100.0 109.47
angle_coeff 1 45.7696 109.47
dihedral_coeff 1 12 -1 2
#improper_coeff 1 5.3 -1 2
#improper_coeff 1 3 1 2

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

minimize 1.0e-15 1.0e-15 1000 100000
velocity water create 300.0 12345 temp water_temp
velocity graphene create 300.0 12345 temp graphene_temp

#fix 1 water shake 1.0e-8 100 0 b 1 a 1
#fix 2 graphene setforce 0.0 0.0 0.0

#fix 3 all nvt temp 300.0 300.0 100.0
#fix 3 all nve
#fix 3 all npt temp 300.0 300.0 100.0 iso 1.01325 1.01325 100

fix 2 water nvt temp 300.0 300.0 100.0
fix_modify 2 temp water_comtemp
fix 3 graphene nvt temp 300.0 300.0 100.0
fix_modify 3 temp graphene_temp
fix 4 graphene momentum 1 linear 1 1 1
fix 31 water shake 0.001 20 1000000 b 1 a 1

timestep 0.01
thermo 50
thermo_style one

write_data data.merge1 pair ij
dump 1 all xyz 1 graphene1.xyz
dump_modify 1 element C H O

run 1000

I will greatly appreciate your help.

Best Regards,

Baig Abdullah Al Muhit
PhD student/Graduate Teaching Assistant
Department of Civil and Environmental Engineering
School of Engineering
Vanderbilt University, Nashville, TN

graphene-water.odg (419 KB)

in.graphenemdtemp (2.25 KB)

Hello everyone,
I am building a model for graphene/water system. I used VMD’s nanobuilder to create the graphene system (540 atoms), and topptools to create water box (360 molecules). I merged the simulation boxes of graphene and water using awk and made LAMMPS data file. I have attached the image for initial geometry.

I am trying to run an equibration with minimize command. The temperatures kept increasing whatever timestep I use. I used 1, 0.1, 0.01, and 0.001 timesteps. For the 1-46 runs, temperature is 0 and after that temperatures kept increasing. I used high amount of damping. I am using NVT with shake command. It showed me the same results when I used NVE. Here is my input file:

water with graphene

echo screen
log debug.log

units real
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
#improper_style cvff

pair_style lj/cut/coul/long 8
kspace_style ewald 1.0e-6

neighbor 2.0 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.mergenewtemp
pair_modify mix arithmetic tail yes

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

set group oxygen charge -0.82
set group hydrogen charge 0.41

#pair_coeff 3 3 0.4396 3.851
pair_coeff 3 3 0.12 3.2963
pair_coeff 2 2 0.15535 3.166
#pair_coeff 2 3 0.392 3.19
pair_coeff 1 1 0.0 0.0
pair_coeff 1 2 0.0 0.0
#pair_coeff 1 3 0.129 2.801
pair_coeff 1 3 0.0 0.0

#bond_coeff 2 702.505 1.472
bond_coeff 2 469 1.4
#bond_coeff 1 1000.00 1.000
bond_coeff 1 554.135 1.000
#angle_coeff 2 80 115
angle_coeff 2 85 120
#angle_coeff 1 100.0 109.47
angle_coeff 1 45.7696 109.47
dihedral_coeff 1 12 -1 2
#improper_coeff 1 5.3 -1 2
#improper_coeff 1 3 1 2

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

minimize 1.0e-15 1.0e-15 1000 100000
velocity water create 300.0 12345 temp water_temp
velocity graphene create 300.0 12345 temp graphene_temp

#fix 1 water shake 1.0e-8 100 0 b 1 a 1
#fix 2 graphene setforce 0.0 0.0 0.0

#fix 3 all nvt temp 300.0 300.0 100.0
#fix 3 all nve
#fix 3 all npt temp 300.0 300.0 100.0 iso 1.01325 1.01325 100

fix 2 water nvt temp 300.0 300.0 100.0
fix_modify 2 temp water_comtemp
fix 3 graphene nvt temp 300.0 300.0 100.0
fix_modify 3 temp graphene_temp
fix 4 graphene momentum 1 linear 1 1 1
fix 31 water shake 0.001 20 1000000 b 1 a 1

timestep 0.01
thermo 50
thermo_style one

write_data data.merge1 pair ij
dump 1 all xyz 1 graphene1.xyz
dump_modify 1 element C H O

run 1000

I will greatly appreciate your help.

Best Regards,

Baig Abdullah Al Muhit
PhD student/Graduate Teaching Assistant
Department of Civil and Environmental Engineering
School of Engineering
Vanderbilt University, Nashville, TN

graphene-water.odg (419 KB)

in.graphenemdtemp (2.25 KB)