# Position restraints and barostat in alchemical free energy double-system/single-box setup

**URL:** <https://gromacs.bioexcel.eu/t/position-restraints-and-barostat-in-alchemical-free-energy-double-system-single-box-setup/8104>\
**Category:** User discussions\
**Tags:** free-energy, restraints, pmx\
**Created:** [January 22, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/position-restraints-and-barostat-in-alchemical-free-energy-double-system-single-box-setup/8104 "2024-01-22T10:45:10Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![burunduk](https://avatars.discourse-cdn.com/v4/letter/b/4bbf92/32.png) [@burunduk](https://gromacs.bioexcel.eu/u/burunduk)\
**Post date:** [January 22, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/position-restraints-and-barostat-in-alchemical-free-energy-double-system-single-box-setup/8104/1 "2024-01-22T10:45:10Z")

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GROMACS version: 2023.2  
GROMACS modification: plumed\_2.10.0\_dev

I’m performing calculation protein stability change upon charge modifying mutation. For this reason, I prepared a double-system/single-box setup to maintain constant charge. As suggested in the related chapter, I’m applying position restraints to the COM atom for each of the two protein copies. At the equilibration stage, I get the following warnings, depending on a barostat I use:

For **Parrinello-Rahman**

> 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 to use Berendsen  
> pressure coupling instead.

For **Berendsen**

> The Berendsen barostat does not generate any strictly correct ensemble,  
> and should not be used for new production simulations (in our opinion).  
> We recommend using the C-rescale barostat instead.

And no barostat-related warning for C-rescale.  
So, which is the better choice of barostat for this type of calculations?

Thank you in advance,  
Sofya

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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:** [January 23, 2024, 11:16am UTC](https://gromacs.bioexcel.eu/t/position-restraints-and-barostat-in-alchemical-free-energy-double-system-single-box-setup/8104/2 "2024-01-23T11:16:56Z")

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We would always advice to use the C-rescale barostat.

We forgot to update this error message when deprecating the Berendsen barostat.

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**Author:** ![burunduk](https://avatars.discourse-cdn.com/v4/letter/b/4bbf92/32.png) [@burunduk](https://gromacs.bioexcel.eu/u/burunduk)\
**Post date:** [January 23, 2024, 11:27am UTC](https://gromacs.bioexcel.eu/t/position-restraints-and-barostat-in-alchemical-free-energy-double-system-single-box-setup/8104/3 "2024-01-23T11:27:15Z")

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Thank you!