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LDH modeling issues regarding

Dear Community Members
Help me learn the aspects.
To model the LDH loaded drugs, I followed the following steps.

  1. Brusite is imported
  2. Mg2+ ions are substitutedpartially with Aluminum
  3. Drug is inserted
    But, the drug is inserted on the top of Mg ions. Looking for the guidelines to place it in right place.
    Similarly, looking for the guidance to proceed with the Simulations. Other than Gromacs, which othe software tool is ideal.

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I would suggest breaking or enlarging the unit cell and then moving the molecules with the manipulate tool when you copy/paste or insert.

Finding the “right place” sounds like a job for the calculation (e.g., LAMMPS).

For materials, I would generally recommend LAMMPS or GULP over Gromacs, which is more for biomolecular systems.

When you paste your drug molecule, it should be selected, so using the manipulate tool you can move and rotate it. If you make a bond between LDH and the drug, then you can do structure relaxation with the optimize tool (I guess it is better to freeze LDH).

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