# Protein Ligand complex MD simulation (Multiple protein chain in the same box)

**URL:** https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation-multiple-protein-chain-in-the-same-box/7020
**Category:** User discussions
**Tags:** mdrun
**Created:** [August 14, 2023, 6:27am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation-multiple-protein-chain-in-the-same-box/7020 "2023-08-14T06:27:05Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![Tanvir](https://avatars.discourse-cdn.com/v4/letter/t/e99b99/32.png) [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [August 14, 2023, 6:27am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation-multiple-protein-chain-in-the-same-box/7020/1 "2023-08-14T06:27:05Z")

</div>

GROMACS version: 2023.2

I am using Gromacs to conduct MD simulation. The protein chain I am utilizing contains two chains. And it is necessary to retain both chains, as they both contain crucial conformational sites. When I use both chains, however, I obtain very unconventional results, whereas when I use a single chain, I obtain conventional results. I have reviewed every file and methods. But was unable to solve it. For protein topolgy, I used the charmm36 force field. And CGenFF server was used to generate ligand topology. Can anyone please help to solve the error ?  
First Figure - Both protein Chains  
Second Figure - Only one protein Chain.

 ![fig1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1f08e471f3501f4d8f1f0055a510b63dbca3de9d.jpeg)  
 ![fig2](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/148defc9e7d1345ba88ba47b2caf5d54a0c4d29a.jpeg)