# MD of multiple ligands with charmm36 force field

**URL:** https://gromacs.bioexcel.eu/t/md-of-multiple-ligands-with-charmm36-force-field/5543
**Category:** User discussions
**Created:** [January 10, 2023, 9:22am UTC](https://gromacs.bioexcel.eu/t/md-of-multiple-ligands-with-charmm36-force-field/5543 "2023-01-10T09:22:51Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![aysebercinb](https://avatars.discourse-cdn.com/v4/letter/a/5daacb/32.png) [@aysebercinb](https://gromacs.bioexcel.eu/u/aysebercinb)
#### Post date: [January 10, 2023, 9:22am UTC](https://gromacs.bioexcel.eu/t/md-of-multiple-ligands-with-charmm36-force-field/5543/1 "2023-01-10T09:22:51Z")

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GROMACS version: 2020.4

Hello,

I am working on a protein-ligand complex and I am performing MD simulations of this complex using the force field charmm36-jul2021. I am also using the default cgenff parameters in the force field files for ligand parametrization.

This complex has 2 ligands and the aromatic rings are well aligned in the x-ray structures. However, after starting the simulation this alignment is disrupted. How can I keep this conformation during the simulation? I think this is due to the lack of force field parameters for ligand-ligand interactions. What is the best solution for this situation?

Thanks in advance,  
Berçin

 ![starting_conformation](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/edbdfba6bc0bb808df859d09c51d7e98b85d3d3c.jpeg)  
 ![after_MD](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c270beaf1f6b264e4c169bbb506b500dfaca3297.jpeg)

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### Author: ![Chongee](https://avatars.discourse-cdn.com/v4/letter/c/ce73a5/32.png) [@Chongee](https://gromacs.bioexcel.eu/u/Chongee)
#### Post date: [January 14, 2025, 5:14pm UTC](https://gromacs.bioexcel.eu/t/md-of-multiple-ligands-with-charmm36-force-field/5543/2 "2025-01-14T17:14:40Z")

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Have you found a solution? Were there any issues with how you’ve defined your system? I mean do we have to specifically tell GROMACS to do ligand-ligand interactions? Or have you tried a different force field?  
I know that you’ve posted this more than a year ago, but I am just about to use GROMACS with CHARMM36 and my protein also has 2 ligands. I’m not too concerned about ring-ring interactions, but still interested in general.