Dummy atoms in EMC

[sknippen]

Following the instructions on TIP5P via

How to model a TIP5P water molecule?

You can define TIP5P molecules with a molecule file and then populate your simulation box with them using create_atoms. You can then simulate the water molecules as rigid objects using fix rigid or fix rigid/small (or their thermostatted/barostatted variants). To avoid LAMMPS erroring out, you need to assign a tiny mass to the “massless” sites, but if those masses are small enough, they won’t make a difference (thanks to the truncation of floating point math). TIP4P is a special case, since one…

and the parameters in
DOI: 10.1021/acs.jpcb.9b03149
(Zhao et al., J Phys Chem B 123 (2019), 4594),
I could reconstruct the tip7p.mol:

–

Water molecule. Explicit TIP7P geometry for use with fix rigid

7 atoms

Coords

1 0.00000 0.00000 0.00000
2 0.75695 0.58588 0.00000
3 -0.75695 0.58588 0.00000
4 0.00000 -0.40415 0.57154
5 0.00000 -0.40415 -0.57154
6 0.37848 0.292940 0.000000
7 -0.37848 0.292940 0.000000

Types

1 1 # O
2 2 # H
3 2 # H
4 3 # L
5 3 # L
6 4 # M
7 4 # M

Charges

1 0.1110
2 0.5801
3 0.5801
4 -0.1772
5 -0.1772
6 -0.4584
7 -0.4584

… and the in.tip7p:

–
units real
atom_style charge
atom_modify map array
region box block 4.12 62.05 4.12 62.05 4.12 62.05
create_box 4 box

mass 1 15.9994
mass 2 1.008
mass 3 1.0e-100
mass 4 1.0e-100

pair_style lj/cut/coul/long 10.0
pair_coeff 1 1 0.150 3.156
pair_coeff 2 2 0.003 1.448
pair_coeff 3 3 0.0 1.0
pair_coeff 4 4 0.0 1.0

kspace_style pppm 1.0e-5

fix mol all property/atom mol ghost yes
molecule water tip7p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33

timestep 0.2
fix rigid all rigid/nvt/small molecule temp 300.0 300.0 10.0
velocity all create 300.0 5463576

thermo_style custom step temp press etotal pe ke
thermo 500
run 5000
write_data bunch_of_water_tip7p.data