How to Include Parameters for Neutral Copper Atoms in GROMACS Force Field for MD Simulations?

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1

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Dear GROMACS users,

I need to perform MD simulations of Cu nanoparticles using GROMACS. I have created an .itp file for Cu with the following content:

[ moleculetype ]
; Name nrexcl
cu 1

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CU 1 CU CU 1 2.0 63.546


However, I am encountering an error: `Atomtype CU not found`. The existing GROMACS `.itp` files only include data for Cu (+1) and Cu (+2) ions, not for the neutral Cu atom. Additionally, the `.itp` files are read-only, so I cannot add the data for neutral Cu.

How can I resolve this issue?
2

Given that you’ve created a .itp file, you should be able to include the parameters in your topol.top with an #include command (you can refer to this Protein-Ligand Complex for an example).

If you don’t have a starting topol.top, you can convert the .itp file into one by including whatever #include commands you need to call on your forcefield, or just generate one from a .pdb file you already know works and then replace the molecules in that file with the ones you actually want.

3

Dear @Karis,
I followed your instructions. Now its working. Thank you for ypur assistance

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