# Choice of Barostat during NPT equilibration

**URL:** <https://gromacs.bioexcel.eu/t/choice-of-barostat-during-npt-equilibration/9396>\
**Category:** User discussions\
**Created:** [June 14, 2024, 8:12pm UTC](https://gromacs.bioexcel.eu/t/choice-of-barostat-during-npt-equilibration/9396 "2024-06-14T20:12:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ligand1](https://avatars.discourse-cdn.com/v4/letter/l/278dde/32.png) [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\
**Post date:** [June 14, 2024, 8:12pm UTC](https://gromacs.bioexcel.eu/t/choice-of-barostat-during-npt-equilibration/9396/1 "2024-06-14T20:12:39Z")

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GROMACS version: 2022.5  
GROMACS modification: No

Hi,

I am trying to simulate a protein-ligand complex embedded in the POPC bilayer. I have generated my system using CHARMM-GUI. While I am trying to start the for NPT equilibration of my system I am getting the following NOTE from Gromacs:

NOTE 2 [file topol.top, line 34]:  
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.

After some reading online I understand that Berendsen pressure coupling might not be the appropriate way to proceed.

I am using the following settings in my mdp file:

tcoupl = Nose-Hoover  
tc\_grps = Protein\_GDS\_POPC Solvent  
tau\_t = 1.0 1.0  
ref\_t = 303.15 303.15  
;  
pcoupl = Parrinello-Rahman  
pcoupltype = semiisotropic  
tau\_p = 5.0  
compressibility = 4.5e-5 4.5e-5  
ref\_p = 1.0 1.0  
refcoord\_scaling = com

I have gone through multiple tutorials available on the internet. I see mostly Parrinello-Rahman pressure coupling is used (including the one in tutorial written by @jalemkul . I am a bit confused and need some advice.

Thanks in advance

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**Author:** ![Dulaj](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dulaj/32/3408_2.png) [@Dulaj](https://gromacs.bioexcel.eu/u/Dulaj)\
**Post date:** [June 14, 2024, 8:24pm UTC](https://gromacs.bioexcel.eu/t/choice-of-barostat-during-npt-equilibration/9396/2 "2024-06-14T20:24:52Z")

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When the system is not in a well-equilibrated state, a second order pressure coupling such as Parinnello Rahman can not be used. C-rescale will be most appropriate one. I don’t know C-rescale is available on your Gromacs version since C-rescale is very new.

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**Author:** ![Ligand1](https://avatars.discourse-cdn.com/v4/letter/l/278dde/32.png) [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\
**Post date:** [June 14, 2024, 11:12pm UTC](https://gromacs.bioexcel.eu/t/choice-of-barostat-during-npt-equilibration/9396/3 "2024-06-14T23:12:34Z")

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Hi Dulaj

Many thanks for replying to my post. I did not mention (and I am sorry for that) in my earlier post that I already did around 5 ns of NVT equilibration with my system. My system is fairly stable with no warnings or collapse. Its just that I have the position restrains turned on.

So according to your suggestion can I modify the follows in my mdp file:

pcoupl = C-rescale  
pcoupltype = semiisotropic

Thanks