EAM Au in SPC/E water: bonds and special bonds

LAMMPS LAMMPS General Discussion
1

Hello LAMMPS community,
I am trying to create a system of equilibrated non-flexible SPC/E water with an embedded EAM Au nanoparticle. The Au-O interaction is described by 6-12 LJ. My question is how to properly handle bonds and special bonds. LAMMPS warning message says: “The exclusion settings will eliminate neighbors in the neighbor list, which the many-body potential needs to calculate its terms correctly.” Do I understand it correctly that the O and H atoms that have bonds between them are not interacting with Au atoms in my setup?
The part of my script where I set up simulation:

<......>
pair_style	lj/cut/coul/long 9.0 9.0
special_bonds   lj/coul 0.0 0.0 0.5

bond_style	harmonic
angle_style	harmonic
dihedral_style	none
improper_style	none
read_data water_20nm.dat extra/atom/types 1

##########__Technical part where I create the nanoparticle__####
region to_del_inner sphere ${x_cent} ${y_cent} ${z_cent} ${R_Au_del} side in units box
region to_create_Au sphere ${x_cent} ${y_cent} ${z_cent} ${R_Au} side in units box
delete_atoms region to_del_inner mol yes
lattice fcc 4.1464

create_atoms 3 region to_create_Au

mass 3 196.966569
########__The part is over__#############

pair_style hybrid eam/alloy lj/cut/coul/long 9.0 lj/cut 9.0

pair_coeff * * eam/alloy Au-W1266.v1.eam.alloy NULL NULL Au #Au - Au
pair_coeff 1 1 lj/cut/coul/long 0.15539421659476232 3.16555789 #O-O
pair_coeff 1 2 lj/cut 0.0000 0.0000 # O-H
pair_coeff 2 2 lj/cut 0.0000 0.0000 #H-H
pair_coeff 2 3 lj/cut ${epsHAu} ${sigmaHAu}# Au-H
pair_coeff 1 3 lj/cut ${epsOAu} ${sigmaOAu}# Au-O

pair_modify tail yes
kspace_style	pppm 1.0e-4

bond_coeff	1 5000.00 1.000
angle_coeff	1 500.0 109.47
reset_ids
neighbor        2.0 bin
neigh_modify	every 1 delay 10 check yes
<......>

Thank you!

2

No. For as long as you do not have any bonds that include any Au atoms (i.e. atom type 3), you have nothing to worry about.

The processing of exclusions means that non-bonded interactions that also have a bonded interaction (i.e. are a so-called 1-2, 1-3, or 1-4 pair in the bond topology) will be removed from the neighbor list (or scaled). So this would apply only to the intra-molecular non-bonded interactions between the atoms within the water atoms. Those are irrelevant anyway since you are keeping them rigid with fix shake. For more details you should read up on the topic in an MD text book that explains how molecular force fields are derived.