# Protein-Protein simulation where one protein is a trimer
**URL:** https://gromacs.bioexcel.eu/t/protein-protein-simulation-where-one-protein-is-a-trimer/7251
**Category:** User discussions
**Created:** [September 23, 2023, 5:32am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation-where-one-protein-is-a-trimer/7251 "2023-09-23T05:32:09Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@JIQuiambao](https://gromacs.bioexcel.eu/u/JIQuiambao)
#### Post date: [September 23, 2023, 5:32am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation-where-one-protein-is-a-trimer/7251/1 "2023-09-23T05:32:09Z")
GROMACS version: 2023.2
GROMACS modification: No
Here post your question
Good day!
I would like to simulate a protein-protein system involving a death receptor-death ligand system. Death receptors typically trimerize when they recognize the approach of a death ligand. I ran one MD simulation and found that in the output file, only a monomer and the ligand was simulated and not the whole trimer. I followed the protein-ligand tutorial by Mr. Justin A. Lemkul, Ph.D. I was wondering if there is a way to simulate the whole trimer + ligand or would the output be just the monomer + ligand if the individual monomers that make up the trimer have the same sequence of amino acids.
I really appreciate any input in this. Thank you in advance!
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 23, 2023, 6:41pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation-where-one-protein-is-a-trimer/7251/2 "2023-09-23T18:41:46Z")
The output of the simulation is based on whatever the input is. Simulate a monomer, get a monomer. Simulate a trimer, get a trimer.
Note that the protein-ligand tutorial is designed for non-protein ligands. You should not follow its protocol for a protein that is a binding partner/ligand. `pdb2gmx` can handle writing the entire topology for a multi-chain system.