# The combination of restraints and Parrinello-Rahman for md run

**URL:** <https://gromacs.bioexcel.eu/t/the-combination-of-restraints-and-parrinello-rahman-for-md-run/9808>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun\
**Created:** [August 3, 2024, 2:25pm UTC](https://gromacs.bioexcel.eu/t/the-combination-of-restraints-and-parrinello-rahman-for-md-run/9808 "2024-08-03T14:25:21Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![fatemeh](https://avatars.discourse-cdn.com/v4/letter/f/9de053/32.png) [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\
**Post date:** [August 3, 2024, 2:25pm UTC](https://gromacs.bioexcel.eu/t/the-combination-of-restraints-and-parrinello-rahman-for-md-run/9808/1 "2024-08-03T14:25:22Z")

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GROMACS version:gromacs2023.2  
GROMACS modification: Yes/No  
@hess @jalemkul  
Hello,

I applied position restraints (Flat-bottomed position restraints) on two atoms of DNA and ran MD (300 ns) for data collection. I received this note while running grompp:  
“You are combining position restraints with Parrinello-Rahman pressure coupling, which can lead to instabilities. If you really want to combine position restraints with pressure coupling, we suggest using Berendsen pressure coupling instead.”  
The system did not crash or blow up. Can I trust the data, or is it recommended to repeat the simulation with c-rescale instead?  
If I want to use c-rescale, should I change any other parameters in the MDP file accordingly?  
thank you in advance for your help.  
Best regards

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [August 6, 2024, 1:42pm UTC](https://gromacs.bioexcel.eu/t/the-combination-of-restraints-and-parrinello-rahman-for-md-run/9808/2 "2024-08-06T13:42:52Z")

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If you simulations ran fine, there is no issue.

If you want to use c-rescale, we recommend a value of tau\_t of 1 ps.

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**Author:** ![fatemeh](https://avatars.discourse-cdn.com/v4/letter/f/9de053/32.png) [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\
**Post date:** [August 8, 2024, 1:16pm UTC](https://gromacs.bioexcel.eu/t/the-combination-of-restraints-and-parrinello-rahman-for-md-run/9808/3 "2024-08-08T13:16:22Z")

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> [@hess](#):
>
> If you simulations ran fine, there is no issue.

thank you so much.  
I highly apricate your assistance.  
Best regards,  
Fatemeh,