[gmx-users] Input GRO file for a calcite crystal slab (meant for use in adsorption study)

[Anuradha Bhat]

Hi GMX-Users,

I am  trying to study the adsorption of a certain molecule on the surface
of calcite. To that end, I have created a triclinic box containing a slab
of calcite crystal and vacuum over the slab. I created this box using
Atomic Simulation Environment (ASE). The top surface of the slab (i.e.,
surface with normal pointing in the +z direction) has Miller Indices of
(104), which is known to be the most stable surface of calcite according to
literature.

When I viewed the structure in VMD, I found that, close to the xz and yz
faces of the box, the carbonate groups were split/broken between two
neighboring boxes. Moreover, in the GRO file of the box that I had created
using ASE, there was only one residue (which ASE labelled as DUM) and all
atoms were shown to belong to it. I am pasting a portion of the GRO file:

A Gromacs structure file written by ASE

 4950

    1DUM     Ca    1   2.092   0.041   0.079  0.0000  0.0000  0.0000

    1DUM     Ca    2   0.763   0.041   0.079  0.0000  0.0000  0.0000

    1DUM      C    3   0.099   0.041   0.079  0.0000  0.0000  0.0000

    1DUM      C    4   1.427   0.041   0.079  0.0000  0.0000  0.0000

    1DUM      O    5  -0.000   0.070   0.000 -0.0000  0.0000  0.0000

    1DUM      O    6   2.136   0.262   0.000  0.0000  0.0000  0.0000

    1DUM      O    7  -0.044   0.388   0.079 -0.0000  0.0000  0.0000

    1DUM      O    8   1.708   0.226   0.000  0.0000  0.0000  0.0000

    1DUM      O    9   1.378   0.161   0.079  0.0000  0.0000  0.0000

    1DUM      O   10   1.186   0.417  -0.000  0.0000  0.0000 -0.0000

    1DUM      O   11   0.758   0.382   0.000  0.0000  0.0000  0.0000

    1DUM      O   12   0.428   0.106   0.000  0.0000  0.0000  0.0000

    1DUM     Ca   13   2.471   0.196   0.079  0.0000  0.0000  0.0000

    1DUM     Ca   14   0.192   0.352   0.079  0.0000  0.0000  0.0000

    1DUM     Ca   15   1.521   0.352   0.079  0.0000  0.0000  0.0000

    1DUM     Ca   16   2.284   0.393   0.386  0.0000  0.0000  0.0000


Questions:
1) I plan on using a forcefield where carbonate ions will be treated as
rigid molecular entities. I was wondering if the GRO file should be
structured in a manner where the calcium ions and the carbonate ions are
all treated as separate residues?
2) If the answer to the above is yes, then, is there a quick way to parse
the above GRO file into a form where the carbonate ions get CORRECTLY
grouped into the residues?
2b) Would the system then just become equivalent to having a bunch of
calcium and carbonate ions fixed at certain positions, but there would be
no over-arching molecule that unifies them into a lattice?
3) How would I then go about dealing with the carbonates that are broken
across box boundaries? I read somewhere that one would have to set the flag
of periodic-molecules to yes in the mdp file. Would that be applicable here
too?
I would really appreciate your help!

Thank you,
Sincerely,
Anuradha.