Dear all
I generated a pdb file for 256 water molecules using packmol (attached herewith). That pdb file i used to generate lammps data file using topotools 1.2. But when I run lammps it is comming out with the
LAMMPS (18 Jan 2011)
SPC/E water box benchmark
units real
atom_style full
boundary p p p
read_data data.256water
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
2 by 2 by 1 processor grid
768 atoms
512 bonds
256 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
#replicate 2 4 1
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
kspace_modify order 3
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
256 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization …
G vector = 0.246379
grid = 24 24 24
stencil order = 3
RMS precision = 8.83199e-05
brick FFT buffer size/proc = 8381 3456 4437
Memory usage per processor = 4.3544 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 15204.218 0 15661.176 139366.74
ERROR: Out of range atoms - cannot compute PPPM
.
Can u please suggest how to overcome it?
Suggestion will be appriciated.
Regards
MALI
data.256water (53.8 KB)
in.256water (684 Bytes)
log.lammps (1.56 KB)