# Gromacs NPT error

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588>\
**Category:** User discussions\
**Created:** [February 18, 2025, 7:47pm UTC](https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588 "2025-02-18T19:47:27Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![js\_gro](https://avatars.discourse-cdn.com/v4/letter/j/ac8455/32.png) [@js\_gro](https://gromacs.bioexcel.eu/u/js_gro)\
**Post date:** [February 18, 2025, 7:47pm UTC](https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588/1 "2025-02-18T19:47:27Z")

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GROMACS version: 2022  
GROMACS modification: No  
Fatal error:  
DD cell 13 0 0 could only obtain 1356 of the 1357 atoms that are connected via  
constraints from the neighboring cells. This probably means your constraint  
lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order.

I have 80 chains, each containing 40 carbon atoms. Initially, they are all extended. I run minimization followed by a short NVT simulation at 400 K. The simulation box is large. However, when I run NPT at 400 K, I encounter an error.

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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:** [February 19, 2025, 1:46pm UTC](https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588/2 "2025-02-19T13:46:37Z")

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My guess is that you system is not sufficiently equilibrated/minimized. At what step does this happen? Do you get very high kinetic energy / temperatures?

Note that we would like to avoid that users gets such low-level errors, but sometimes this is difficult to avoid.

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<div class="post-metadata">

**Author:** ![js\_gro](https://avatars.discourse-cdn.com/v4/letter/j/ac8455/32.png) [@js\_gro](https://gromacs.bioexcel.eu/u/js_gro)\
**Post date:** [February 19, 2025, 7:27pm UTC](https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588/3 "2025-02-19T19:27:57Z")

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It happens during equilibration. After the NVT step, a large void appears in the simulation, causing a drastic reduction in box size, which leads to an error. Is there a way to remove the Coulombic force for a few timesteps?

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<div class="post-metadata">

**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:** [February 20, 2025, 7:29am UTC](https://gromacs.bioexcel.eu/t/gromacs-npt-error/11588/4 "2025-02-20T07:29:08Z")

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Then I would simply increase tau\_p (a lot), that will make the box shrink slower. This assumes that you are using the c-rescale barostat, which you should for equilibration.