# MD simulation of Docked structures
**URL:** https://gromacs.bioexcel.eu/t/md-simulation-of-docked-structures/10909
**Category:** User discussions
**Tags:** mdp-parameters, mdrun
**Created:** [December 27, 2024, 6:02pm UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-docked-structures/10909 "2024-12-27T18:02:18Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@aaronjacob7](https://gromacs.bioexcel.eu/u/aaronjacob7)
#### Post date: [December 27, 2024, 6:02pm UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-docked-structures/10909/1 "2024-12-27T18:02:18Z")
GROMACS version: 2021.4
GROMACS modification: No
Hello,
I am new to running MD simulations on GROMACS, i need to do analysis of a 2 proteins docked in haddock.
I wanted to ask if the procedure will be same as in the Protein-Ligand tutorial.
I could not find any other resources concerning protein-protein MD simulation.
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 28, 2024, 1:50am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-docked-structures/10909/2 "2024-12-28T01:50:35Z")
Running a simulation of a a protein complex is no different from running a simulation of a single protein. `pdb2gmx` can handle multiple chains in a single PDB file with no problem, as long as each chain has its own chain identifier or they are separated by TER cards.
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### Author:  [@aaronjacob7](https://gromacs.bioexcel.eu/u/aaronjacob7)
#### Post date: [December 30, 2024, 7:16am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-docked-structures/10909/3 "2024-12-30T07:16:25Z")
> [@jalemkul](#):
>
> TER cards.
Thank you sir