# Blow up during NPT equilibration using Berendsen barostat

**URL:** <https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527>\
**Category:** User discussions\
**Tags:** forcefield, mdp-parameters, simulation-setup\
**Created:** [March 6, 2024, 7:56am UTC](https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527 "2024-03-06T07:56:21Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![bahrulabid\_2511](https://avatars.discourse-cdn.com/v4/letter/b/8baadc/32.png) [@bahrulabid\_2511](https://gromacs.bioexcel.eu/u/bahrulabid_2511)\
**Post date:** [March 6, 2024, 7:56am UTC](https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527/1 "2024-03-06T07:56:21Z")

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GROMACS version: 2022.2  
GROMACS modification: No

I simulate molecular dynamics of 1024 water. Water molecule is actually made from quantum calculation using Orca (B3LYP/def2-TZVP) and I set the GAFF from Amber. My simulation consist of minimization; nve, nvt, and npt equilibration; and nvt production. The results of minimization, nve & nvt equilibration seem normal, but when I did npt equilibration, I think my simulation box blew up. I know that normal graph of pressure and volume during npt equilibration is undergoing fluctuation. But the graph of pressure and volume is not fluctuating, it’s exponential graph.

Can anyone help me what actually happen in my simulation? Is it because of force field or something else? Thank you

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**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\
**Post date:** [March 6, 2024, 12:24pm UTC](https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527/2 "2024-03-06T12:24:54Z")

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Your system may need more steps of minimization/nvt. Visually checking may help you understand the issues with the initial structure. It is also better to test other type of barostats. Berendsen barostat is outdated, Parrinello-Rahman is better to utilize ‘only’ in production runs when the structure is ‘properly equilibrated’, but safe option is the c-rescale algorithm.

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**Author:** ![bahrulabid\_2511](https://avatars.discourse-cdn.com/v4/letter/b/8baadc/32.png) [@bahrulabid\_2511](https://gromacs.bioexcel.eu/u/bahrulabid_2511)\
**Post date:** [March 6, 2024, 1:32pm UTC](https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527/3 "2024-03-06T13:32:28Z")

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Thank you for your advice.  
I’ve tried to do twcie minimization: first minimization consists of 1000 steps and the second consists of 50,000 steps. I’ve also tried using c-rescale to change Berendsen. The result doesn’t change anything.

Is there other thing I should do to accomplish this?

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 6, 2024, 4:57pm UTC](https://gromacs.bioexcel.eu/t/blow-up-during-npt-equilibration-using-berendsen-barostat/8527/4 "2024-03-06T16:57:28Z")

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tried rebuilding the system?