Hi ,
I am very new to LAMMPS and trying to calculate diffusion coefficient for molecules using compute msd/molecule command but it give me this warning
WARNING: Atom with molecule ID = 0 included in compute molecule group
and it doesn’t go through anything.
Below is my .inp file
units real
dimension 3
boundary p p p
atom_style full
pair_style lj/cut/coul/long 8.0
pair_modify mix arithmetic
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
kspace_style ewald 0.0001
read_data address/water.data
neighbor 2.0 bin
neigh_modify check yes
#special_bonds 0.0 0.0 1.0
timestep 1.0
run_style verlet
reset_timestep 0
fix 3 all npt 278.0 278.0 100 aniso NULL NULL NULL NULL 1.0 1.0 1000
thermo_style multi
thermo 1000
compute 1 all msd/molecule
fix 1_store_coord all store/coord
dump coords3 all custom 1000 /address/w.xyz id mol type q x y z
run 1000
unfix 3
#undump coords3
That is data file
AMMPS 2005 data file for waterbox
20655 atoms
13770 bonds
6885 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0.000000000 61.29 xlo xhi
0.000000000 60.487 ylo yhi
0.000000000 57.00 zlo zhi
Masses
1 15.999400
2 1.008000
Pair Coeffs
1 0.1521000000 3.15070000000
2 0.0000000000 0.0000000000
Bond Coeffs
1 450.0 0.9572
Angle Coeffs
1 55.0 104.52
Atoms
What would you suggest to avoid this warning.
Thank you so much for your help
Yasaman