How to generate a GROMACS topology (.itp) for a silver nanocluster using the INTERFACE Force Field?

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GROMACS version:
GROMACS modification: Yes/No
Hello everyone,

I am currently having difficulty understanding the correct topology/parameterization workflow for the metal nanocluster.

My system consists of a protein interacting with a metal nanocluster of approximately 6 nm diameter. I would like to use the INTERFACE Force Field (IFF) for the metal nanocluster.

Following a suggestion, I used the CHARMM-GUI Nanomaterial Modeler and selected GROMACS as the target MD engine. The generated GROMACS directory contains files such as:

  • step3_input.gro
  • step3_input.pdb
  • step3_input.psf
  • topol.top
  • toppar/NMA.itp
  • toppar/forcefield.itp
  • toppar/TIP3.itp
  • toppar/SOD.itp
  • toppar/CLA.itp

My main confusion is whether NMA.itp is already the topology for the generated nanocluster, with the required IFF parameters defined in forcefield.itp, or whether I need to combine information from these files to create a separate final metal.itp file.

I have also explored ACPYPE, but I understand that generating parameters through ACPYPE may not necessarily reproduce the INTERFACE Force Field parameterization that I want to use.

Could someone please clarify:

  1. Which of the CHARMM-GUI-generated files contains the actual topology of the Ag nanocluster?
  2. Are the atom types and non-bonded parameters already defined in the generated force-field files?
  3. Should NMA.itp be included directly in topol.top rather than creating another .itp file?
  4. What is the recommended procedure for integrating this IFF-based metal nanocluster topology with a CHARMM36 protein topology in GROMACS?
  5. Are there any additional steps required when using a larger nanocluster with IFF?

I would appreciate any guidance or examples from users who have worked with metal nanoparticles and the INTERFACE Force Field in GROMACS.

I can provide the relevant sections of NMA.itp, forcefield.itp, and topol.top if needed.

Thank you.