GROMACS version: 2023
GROMACS modification: Yes/No
I intend to set up an MgO ionic oxide model with a polarisable O atom according to Dick and Overhauser, with a zero mass shell (O_s) connected to the O core (O_c) via a harmonic spring. I would like to know if the following definition is correct:
[ atomtypes ]
; atom_type at.num mass charge ptype sigma epsilon
Mg2 12 24.30500 0.000 A 0.000000e+00 0.000000 0.000000e+00
O_c 8 15.99940 0.000 A 0.000000e+00 0.000000 0.000000e+00
O_s 8 0.00000 0.000 D 2.196464e+06 67.114094 1.965445e-03
and the core-shell connection is defined under the [ bonds ] directive as follows:
[ bonds ]
…
…
[ bonds ]
; no bond
; core shell funct distance force_constant
13 25 1 0.0000 151870.8906
14 26 1 0.0000 151870.8906
15 27 1 0.0000 151870.8906
16 28 1 0.0000 151870.8906
17 29 1 0.0000 151870.8906
18 30 1 0.0000 151870.8906
19 31 1 0.0000 151870.8906
20 32 1 0.0000 151870.8906
21 33 1 0.0000 151870.8906
…
…
Apparently, there is no issue in setting up a tpr file, but I just want to know is this the correct way to define a core-shell model?