I am trying to use EAM with the hybrid pair_style command, but I get an
error that all pair coeffiecients are not set. I was hoping that
someone could take a quick look at my input script and data file to see
if there are any glaring mistakes. I have tried to specify the pair
coefficients within the data file and the two eam files are located in
my working directory. I am using the ptu3 and the auu3 EAM files
located in the potentials directory in the LAMMPS distribution.
Thanks,
Christina Payne
[email protected]...
Here is the input file...
units real
neigh_modify delay 5 every 1
boundary p p f
atom_style hybrid full eam
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid lj/charmm/coul/long 8 10 eam
pair_modify mix arithmetic
kspace_style pppm 1e-4
kspace_modify slab 3.0
read_data total.data
special_bonds charmm
group platinum type 38
group gold type 39
group mica type 32 33 34 35 36 37 40 41
group water type 1 23
group ions type 31
group dna id <> 1 512
group solution join water ions dna
group surface join mica platinum gold
fix 1 solution nvt 300.0 300.0 100.0
fix 2 all shake 1e-6 500 0 m 1.0 a 61
temperature mobile solution full
velocity all create 300.0 12345678 dist uniform
thermo 1
thermo_style one
thermo_modify temp mobile
timestep 0.0005
restart 10000 restart.equil.a restart.equil.b
dump equil1 all atom 500 dump.atom.equil.1
dump velo1 solution velocity 500 dump.velo.equil.1
run 50000
undump equil1
undump velo1
dump equil2 all atom 500 dump.atom.equil.2.a
dump velo2 solution velocity 500 dump.velo.equil.2.a
timestep 2.0
run 100000
And here is the first part of my data file...
Created by charmm2lammps v1.6.3 on Wed Sep 14 14:28:27 CDT 2005
134208 atoms
56639 bonds
26468 angles
1594 dihedrals
48 impropers
41 atom types
41 bond types
74 angle types
139 dihedral types
6 improper types
-0.698 207.86 xlo xhi
-0.018 144.286 ylo yhi
-50.403 0.846 zlo zhi
Masses
1 1.008 # HT
2 1.008 # HN1
3 1.008 # HN2
4 1.008 # HN3
5 1.008 # HN5
6 1.008 # HN7
7 1.008 # HN8
8 1.008 # HN9
9 12.011 # CN1
10 12.011 # CN1T
11 12.011 # CN2
12 12.011 # CN3
13 12.011 # CN3T
14 12.011 # CN7
15 12.011 # CN7B
16 12.011 # CN8B
17 12.011 # CN9
18 14.007 # NN1
19 14.007 # NN2
20 14.007 # NN2B
21 14.007 # NN2U
22 14.007 # NN3
23 15.9994 # OT
24 15.9994 # ON1
25 15.9994 # ON1C
26 15.9994 # ON2
27 15.9994 # ON3
28 15.9994 # ON5
29 15.9994 # ON6B
30 30.974 # P
31 22.98977 # SOD
32 28.09 # SI
33 26.98 # AT
34 26.98 # AO
35 16 # OB
36 16 # OH
37 1.008 # HO
38 195.08 # PT
39 196.97 # AU
40 39.102 # POTM
41 16 # OTT
Pair Coeffs
1 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HT
2 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN1
3 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN2
4 lj/charmm/coul/long 0.046 1.959977 0.046 1.959977
# HN3
5 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN5
6 lj/charmm/coul/long 0.022 2.351973 0.022 2.351973
# HN7
7 lj/charmm/coul/long 0.028 2.387609 0.028 2.387609
# HN8
8 lj/charmm/coul/long 0.024 2.387609 0.024 2.387609
# HN9
9 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN1
10 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN1T
11 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN2
12 lj/charmm/coul/long 0.09 3.385415 0.09 3.385415
# CN3
13 lj/charmm/coul/long 0.09 3.385415 0.09 3.385415
# CN3T
14 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
# CN7
15 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
# CN7B
16 lj/charmm/coul/long 0.056 3.581413 0.01 3.385415
# CN8B
17 lj/charmm/coul/long 0.078 3.634867 0.01 3.385415
# CN9
18 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN1
19 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2
20 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2B
21 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2U
22 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN3
23 lj/charmm/coul/long 0.1521 3.150574 0.1521 3.150574
# OT
24 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON1
25 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON1C
26 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON2
27 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON3
28 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON5
29 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON6B
30 lj/charmm/coul/long 0.585 3.830864 0.585 3.830864
# P
31 lj/charmm/coul/long 0.0469 2.429926 0.0469 2.429926
# SOD
32 lj/charmm/coul/long 1.8405e-06 3.302027 1.8405e-06
3.302027 # SI
33 lj/charmm/coul/long 1.8405e-06 3.302027 1.8405e-06
3.302027 # AT
34 lj/charmm/coul/long 1.3298e-06 4.271236 1.3298e-06
4.271236 # AO
35 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OB
36 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OH
37 lj/charmm/coul/long 0.0 0.0 0.0 0.0
# HO
38 eam ptu3
# PT
39 eam auu3
# AU
40 lj/charmm/coul/long 0.1 3.33401 0.1 3.33401
# POTM
41 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OTT
Atoms
1 1 30 1.5 29.2210000 70.6800000 -14.4440000 #
P
2 1 27 -0.78 30.0930000 71.1100000 -14.2090000 #
ON3
3 1 27 -0.78 28.3380000 70.8920000 -14.0260000 #
ON3
4 1 26 -0.57 29.4670000 69.5990000 -15.5970000 #
ON2
5 1 16 -0.08 28.5310000 68.5070000 -15.7450000 #
CN8B
..... and so on...