# Using restraints in production MD for Protein-Ligand complex

**URL:** <https://gromacs.bioexcel.eu/t/using-restraints-in-production-md-for-protein-ligand-complex/2824>\
**Category:** User discussions\
**Tags:** grompp, mdrun\
**Created:** [September 17, 2021, 5:51am UTC](https://gromacs.bioexcel.eu/t/using-restraints-in-production-md-for-protein-ligand-complex/2824 "2021-09-17T05:51:10Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Nupur\_Nagar](https://avatars.discourse-cdn.com/v4/letter/n/858c86/32.png) [@Nupur\_Nagar](https://gromacs.bioexcel.eu/u/Nupur_Nagar)\
**Post date:** [September 17, 2021, 5:51am UTC](https://gromacs.bioexcel.eu/t/using-restraints-in-production-md-for-protein-ligand-complex/2824/1 "2021-09-17T05:51:10Z")

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GROMACS version: 2020.5  
GROMACS modification: Yes

Hi  
I am trying to run a simulation for protein-ligand complex according to the Protein-Ligand complex tutorial on [www.mdtutorials.com](http://www.mdtutorials.com). While running the final Production MD I got the following error:

 ![Screenshot from 2021-09-17 10-59-34](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b22ba8fc0477b6f1c38effcb89a94cd8a64a41ba.png)

As far as I understood here we need to provide a .gro file for position restraints. So I provided the npt.gro file with -r option using the following command:

_gmx\_mpi grompp -f md.mdp -c npt.gro -r npt.gro -t npt.cpt -p topol.top -n index.ndx -o md\_500.tpr_

after this I got this warning:

 ![Screenshot from 2021-09-17 11-15-05](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/29beea8cabcc5f46608f4cfb5c5dd9bb6bad614d.png)  
I used -maxwarn 1 option and was able to run the simulation properly.  
However, in literature it is mentioned that restraints are only mentioned upto equilibriation step since for studying dynamics all molecules should be free for motion. If this is right then how can I overcome this error without using -r option and why is GROMACS showing this error?

Regards  
Nupur

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 20, 2021, 5:28pm UTC](https://gromacs.bioexcel.eu/t/using-restraints-in-production-md-for-protein-ligand-complex/2824/2 "2021-09-20T17:28:03Z")

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There should be no restraints in the production phase of the tutorial. If you’re doing something else or making modifications to the provided files, you will have to provide more detail about what you’re doing.