Contents

Import a unit cell structure

atom=import_atom('1xPyro_LeeGuggenheim_1981_centered.pdb'); % Imports a montmorillonite unit cell structure file into matlabs variable space
atom=replicate_atom(atom,Box_dim,[6 4 1]); % Replicate the structure by 6x4 into a clay layer
atom=substitute_atom(atom,Box_dim,6*4*2/3,'Al','Mgo',5.5) % Perform octahedral substitutions, 5.5 is the min dist between octahedral Mg's.

Write a clayff (Cygan, 2004) .gro and .itp file

atom=clayff_atom(atom,Box_dim,'clayff') % Assign the clayff atom types to the atomstruct
write_atom_itp(atom,Box_dim,'MMT_clayff_1.itp',1.25,1.25,'clayff','spc');
write_atom_gro(atom,Box_dim,'MMT_clayff_1'); % Print the clay sheet to a .gro file

Write a interface (Heinz, 2005) .gro and .itp file

atom=interface_atom(atom,Box_dim,'interface') % Assign the interface atom types to the atomstruct
write_atom_itp(atom,Box_dim,'MMT_interface_1.itp',1.25,2.25,'interface','spc');
write_atom_gro(atom,Box_dim,'MMT_interface_1'); % Print the clay sheet to a .gro file

% Is the charge correct?

Published with MATLAB® R2018b