Graphene sheet rolling after minimization

Hello everyone,

I have built a geometry of water (PACKMOL) and graphene (VMD Nanobuilder) together in a simulation box with LAMMPS and read the data with VMD’s Tk-console. I have two layers of graphene on top and bottom of the box with water sandwiched between them. I put 2 angstrom of vacuum between the water-graphene interfaces and 3 angstrom vacuum at the bottom and top of the box. I tested two cases. Firstly, I did not put any vacuum in the x and y directions. After equilibrating the system, the graphene sheets are found to be rolled across the y axis. Secondly, I put 3 angstrom vacuum in x and y directions also. This time, the graphene sheets seemed to be stable but water molecules are traveling into the vacuum in x and y directions. I checked the box dimensions and the highest and lowest coordinates of the atoms in the system. The coordinates of the atoms are contained in the simulation box. I am giving you two images of my system.. First image is my first test. Second image is my second test. I will greatly appreciate any suggestion or direction. 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 10
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.waterlong
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 -0.8476
set group hydrogen charge 0.4238

#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 2 3 0.095 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 2 469 1.4
bond_coeff 1 554.135 1.000
angle_coeff 2 85 120
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 298.0 12345 temp water_temp
velocity graphene create 298.0 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 298.0 298.0 5.0
fix_modify 2 temp water_comtemp
fix 3 graphene nvt temp 298.0 298.0 5.0
fix_modify 3 temp graphene_temp
fix 4 graphene momentum 1 linear 1 1 1
fix 5 water shake 0.001 20 1000000 b 1 a 1
#fix 6 all box/relax iso 1.01325

timestep 0.01
thermo 50
thermo_style one
thermo_modify lost error flush yes

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

run 100000
write_data data.waterlong_equil pair ij

Best Regards,

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

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Hello everyone,

I have built a geometry of water (PACKMOL) and graphene (VMD Nanobuilder)
together in a simulation box with *LAMMPS* and read the data with *VMD's
Tk-console*. I have two layers of graphene on top and bottom of the box
with water sandwiched between them. I put 2 angstrom of vacuum between the
water-graphene interfaces and 3 angstrom vacuum at the bottom and top of
the box. I tested two cases. Firstly, I did not put any vacuum in the x and
y directions. After equilibrating the system, the graphene sheets are found
to be* rolled across the y axis*. Secondly, I put 3 angstrom vacuum in x
and y directions also. This time, the graphene sheets seemed to be stable
but *water molecules are traveling into the vacuum in x and y directions*.
I checked the box dimensions and the highest and lowest coordinates of the
atoms in the system. The coordinates of the atoms are contained in the
simulation box. I am giving you two images of my system.*. First image is
my first test. Second image is my second test*. I will greatly appreciate
any suggestion or direction. Here is my input file:

​this really is a question about the science of your model and not
particularly about LAMMPS​. thus this is a question you should discuss with
your adviser. the fact, that you don't get the behavior that you expected
does not automatically mean, that there is anything wrong in the
simulation, but may just as well indicate, that you don't understand your
model well enough. in any case, you really should discuss with your
adviser. it is not the job of the simulation software (or this mailing list
for this matter), to teach you how to properly construct models for
simulations.

axel.