# How to simulate protein with 2 ligands

**URL:** <https://gromacs.bioexcel.eu/t/how-to-simulate-protein-with-2-ligands/10085>\
**Category:** User discussions\
**Created:** [September 2, 2024, 8:48pm UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-protein-with-2-ligands/10085 "2024-09-02T20:48:57Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![praviteja](https://avatars.discourse-cdn.com/v4/letter/p/47e85d/32.png) [@praviteja](https://gromacs.bioexcel.eu/u/praviteja)\
**Post date:** [September 2, 2024, 8:48pm UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-protein-with-2-ligands/10085/1 "2024-09-02T20:48:57Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Hello all,  
I am new to gromacs, i have a few confusions regarding protein-ligand simulations

“When performing MD simulations on a protein-ligand complex involving a cofactor and a substrate, is it necessary to include the cofactor in each simulation for different substrates? Additionally, how can I effectively isolate and analyze the dynamics of the protein in complex with only one ligand (substrate), excluding the cofactor from the resulting trajectories?”

I request you to clarify the question… Thank you