# Questions about inter domain/chain distance restraint

**URL:** <https://gromacs.bioexcel.eu/t/questions-about-inter-domain-chain-distance-restraint/13536>\
**Category:** User discussions\
**Tags:** restraints\
**Created:** [June 17, 2026, 9:18am UTC](https://gromacs.bioexcel.eu/t/questions-about-inter-domain-chain-distance-restraint/13536 "2026-06-17T09:18:43Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![dwln](https://avatars.discourse-cdn.com/v4/letter/d/a183cd/32.png) [@dwln](https://gromacs.bioexcel.eu/u/dwln)\
**Post date:** [June 17, 2026, 9:18am UTC](https://gromacs.bioexcel.eu/t/questions-about-inter-domain-chain-distance-restraint/13536/1 "2026-06-17T09:18:43Z")

</div>

GROMACS version: 2026.1  
GROMACS modification: No

Hello!

I am running an SMD on a multidomain and quite large protein. I have restrained one residue on one side, and I want to pull form teh other side on two C termini, to make it a physiological as possible. I am afraid that due to the protein size, just pulling on the end residues may destabilise it, so I want to lock in the two domains together with a distance restraint. However, I am struggling to do this. Should I add it as a new pull coordinate, or is there a way I can add it to the topology files in initialization. fyi: this two domains are on seperate chains, so it’s two separate topology files.

I am thinking about flat bottom potential here