[lammps-users] Gold cluster in water molecule media

Dear all,

I am trying to perform a simulation in LAMMPS in which a collection of
gold atoms is surrounded by water molecules, in which I aim to obtain
the temperature and velocity field. An initial coordinate file has
been created for the hybrid system. I have read the LAMMPS manual and
from this, created an input script. I have specified that EAM will be
used for the gold atom and TIP4P for the water atom. The interaction
between metal and water is LJ-like potential(hope I can get some
parameters for this). Only thermal property is investigated and I do
not think that the all-atom style data is needed for my case.

What atom style should I use for the water/metal hybrid system? I have
tried style angle, bond, even molecular, all were reporting errors.

I have specified bonds and angles in the data file ¡­is this right?
Should I also add charges into data file?

The input script is shown below for a hybrid metal/water system:

clear

dimension 3
units metal
boundary p p p

neighbor 0.3 bin
neigh_modify delay 5

atom_style bond

read_data data.nanofluid

pair_style hybrid lj/cut/coul/long/tip4p 2 1 1 1 1.0 1.0 12.0 eam lj/cut 8.0
pair_coeff 1*2 2*1 100.0 3.5 9.0
pair_coeff 3 3 Au_u3.eam
pair_coeff 1*2 3 lj/cut 0.8 1.3

#bond_style harmonic
#angle_style charmm
#bond_coeff 1 450.000000 1.000000
#angle_coeff 1 55.000000 109.470000 0.000000 0.000000

group hydrogen type 1
group oxygen type 2
group gold type 3

group all union hydrogen oxygen gold

fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d

thermo 50
run 1000

Error comes up like this,'pair coefficient not valid for atom style'

Any response will be greatly appreciated.

Kind regards,
Folayo Osekita
MEng Student, Queen Mary, University of London

Dear all,

[...]

What atom style should I use for the water/metal hybrid system? I have
tried style angle, bond, even molecular, all were reporting errors.

have you tried "atom_style full"? TIP4P requires it.

I have specified bonds and angles in the data file ¡­is this right?
Should I also add charges into data file?

you have to.

The input script is shown below for a hybrid metal/water system:

one more comment you are using a "long" pair style for the water,
those are designed to be used in combination with a kspace style,
or else you are missing some part of the coulomb interaction.

cheers,
   axel.

Use atom_style full and see the read_data doc page for
the format of the data file and what per-atom info you need
to specify.

Steve