How to define pair_style in data file

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1

Dear All
I want to define pair_modify mix arithmetic in data file. what do i do?
I have 37 atom type, that 36 atom types are related to protein-water and 37th is related to gold.
My input file and data file are as follow. when I run system give me the follow error

Input file:

units real
neigh_modify delay 2 every 1

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

pair_style hybrid lj/charmm/coul/long 8 10 eam

read_data

pair_modify mix arithmetic
kspace_style pppm 1e-4
group gold type 37
special_bonds charmm

minimize …
…

Data file:

…
…

Pair Coeffs

1 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
2 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
3 lj/charmm/coul/long 0.022 2.351973 0.022 2.351973
4 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
5 lj/charmm/coul/long 0.03 2.420037 0.03 2.420037
6 lj/charmm/coul/long 0.022 2.351973 0.022 2.351973
7 lj/charmm/coul/long 0.046 1.603618 0.046 1.603618
8 lj/charmm/coul/long 0.0078 2.615679 0.0078 2.615679
9 lj/charmm/coul/long 0.11 3.563595 0.11 3.563595
10 lj/charmm/coul/long 0.07 3.550053 0.07 3.550053
11 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
12 lj/charmm/coul/long 0.055 3.875409 0.01 3.385415
13 lj/charmm/coul/long 0.08 3.670503 0.01 3.385415
14 lj/charmm/coul/long 0.05 3.207235 0.05 3.207235
15 lj/charmm/coul/long 0.05 3.207235 0.05 3.207235
16 lj/charmm/coul/long 0.09 3.207235 0.09 3.385415
17 lj/charmm/coul/long 0.07 3.550053 0.07 3.550053
18 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
19 lj/charmm/coul/long 0.055 3.875409 0.01 3.385415
20 lj/charmm/coul/long 0.055 3.875409 0.01 3.385415
21 lj/charmm/coul/long 0.07 3.563595 0.07 3.563595
22 lj/charmm/coul/long 0.2 3.296325 0.0001 3.296325
23 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
24 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
25 lj/charmm/coul/long 0.2 3.296325 0.2 2.761786
26 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
27 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
28 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
29 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
30 lj/charmm/coul/long 0.12 3.029056 0.12 2.494516
31 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
32 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
33 lj/charmm/coul/long 0.1521 3.150574 0.1521 3.150574
34 lj/charmm/coul/long 0.45 3.563595 0.45 3.563595
35 lj/charmm/coul/long 0.0469 2.429926 0.0469 2.429926
36 lj/charmm/coul/long 0.15 4.04468 0.15 4.04468
37 eam Au_u3.eam

…
…

output of terminal:

LAMMPS (31 Oct 2010)
Scanning data file …
4 = max bonds/atom
6 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
Reading data file …
orthogonal box = (-71.8135 -31.72 -54.1644) to (36.5675 76.661 64.0694)
1 by 1 by 1 processor grid
137950 atoms
92841 bonds
49840 angles
7160 dihedrals
440 impropers
Finding 1-2 1-3 1-4 neighbors …
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
6 atoms in group gold
WARNING: Resetting reneighboring criteria during minimization
PPPM initialization …
G vector = 0.261
grid = 54 54 60
stencil order = 5
RMS precision = 7.53047e-05
brick FFT buffer size/proc = 233227 174960 41772
ERROR on proc 0: All pair coeffs are not set
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

The Best,
Meisam

2

I imagine the ones that are not set are the cross terms
between EAM and the LJ styles. That can't be done
by mixing (what would that mean?), you have to explicitly
specify it in your input script.

Steve

3

Dear Steve
Thanks for your reply. I want to use follow command only for protein elements:

pair_modify mix arithmetic
is it false?

The Best,
Meisam

4

Dear Steve
Thanks for your reply. I want to use follow command only for protein
elements:

pair_modify mix arithmetic

is it false?

that depends on the force field. different ones have different mixing
rules, but the real problem is that you will also need
"cross" interactions between your gold and the rest
and due to using a hybrid pair style, those _cannot_
be derived from mixing. you have to explicitly state
them using pair_coeff statements. i personally don't
like setting (only) per atom type parameters at all,
so i _always_ set _all_ parameters via pair_coeff
commands. much easier to stay consistent this way.

cheers,
    axel.

5

You can use the pair mix for the protein portion,
but as Axel says, you also need the cross terms
between the protein and EAM atoms (metal?).

Steve

6

Dear Steve,
I didn’t find way that i can use pair_modify for a group (There is no option for group in Pair_modify command).
can you guide me?

Sincerely,
Meisam

7

There is none. You have to use pair_coeff and compute the mixed coefficients yourself.

Axel

8

Thank alot

Sincerely,
Meisam