Hi all,
I’m new lammps user, problems confusing me.
In this simple simulation, 298K,NVT,Bulk SPC water diffusion.
I use Material Studio to get *.car and .mdf, than use the tool msi2lmp to make data file(.lammps05).
Here is my input file:
units real
dimension 3
newton on
boundary p p p
atom_style full
neighbor 1.0 bin
neigh_modify delay 5
read_data water333.lammps05
mass 1 15.9994
mass 2 1.008
bond_style harmonic
bond_coeff 1 450 1.000
angle_style harmonic
angle_coeff 1 55 109.47
pair_style lj/cut/coul/cut 9.0 9.0
pair_coeff 1 1 0.1553 3.166 9.0
pair_coeff 1 2 0.0 0.0 0.0
pair_coeff 2 2 0.0 0.0 0.0
group water type 1 2
minimize 1.0e-4 1.0e-6 100 1000
velocity all create 298 5929569 dist uniform
fix fixshake water shake 0.0001 20 0 b 1 a 1
fix nvt all nvt temp 298 298 10
fix temp all temp/berendsen 298 298 10
timestep 1
thermo_style custom step temp etotal vol
thermo_modify lost warn
thermo 1000
run 4000000
dump 1 all dcd 10000 nvt2.dcd
dump_modify 1 unwrap yes
run 4000000
begining of my data file(*.lammps05):
LAMMPS 2005 data file for water333
1620 atoms
1080 bonds
540 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0.000000000 30.000000000 xlo xhi
0.000000000 30.000000000 ylo yhi
0.000000000 30.000000000 zlo zhi
Atoms
1 0 1 -0.820000 2.987002777 1.859785391 7.250709245
2 0 1 -0.820000 5.391468343 3.149880719 7.000222127
3 0 1 -0.820000 7.318925714 3.029318917 1.357676302
4 0 1 -0.820000 3.789862709 3.557045220 5.394744841
5 0 1 -0.820000 1.832659972 3.035141537 3.162750721
…
Now the problem is:
Although I use unwrap to release the water molecules, the molecule didn’t get out the simulation box(30,30,30),It’s not logical.
Hope you can help me.Thank you.
Best wishes!
Hugh
water333.lammps05 (165 KB)