# Update groups can not be used for this system because atoms that are (in)directly constrained togeth **URL:** \ **Category:** User discussions\ **Created:** [May 7, 2024, 2:22pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090 "2024-05-07T14:22:37Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [May 7, 2024, 2:22pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/1 "2024-05-07T14:22:37Z")
GROMACS version: 2023.3 GROMACS modification: No I have coarse-grained an atomistic system (CHARMM36 FF) and using MARTINI 2.2 FF. I often encounter the following error after mdrun: `Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms` Going through the Gromacs mailing list, this error appears when hydrogens bonded to a heavy atom do not appear after the heavy atom in the topology file ([link1](https://gromacs.bioexcel.eu/t/mdrun-randomly-performs-incredibly-slowly-2ns-day-when-its-usually-achieving-300ns-day/6987) and [link2](https://gromacs.bioexcel.eu/t/gpu-update-giving-error-with-protein-ligand-complex/5925)). I have two questions here: 1. I do not have any hydrogens in the CG model and several beads are attached to multiple other beads (upto 3 beads). Most of the bonds are defined as type 1 bonds while some are defined either as type 10 bonds or as type 1 constraints. The molecule is periodic in nature and `periodic-molecules=yes` is entered in mdp file. How can I circumvent this error? 2. My system usually blows up within 100 ns simulation. I perform minimization and then step-wise equilibration using Berendsen and then Parinello-Rahman barostat, increasing timestep from 2 fs to 5, 10 with Berendsen and finally 15 fs with P-R. Then, the production run with P-R barostat and 15 fs time step. I was wondering if the system is blowing up due to the error in point 1 above? Thanks for your help. Regards, Raman ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 7, 2024, 4:19pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/2 "2024-05-07T16:19:42Z")
You shouldn’t interpret that message as an error - I assume that the simulation continues. That is just to inform you that some performance optimizations might not be possible, see [https://manual.gromacs.org/current/release-notes/2019/major/performance.html#implemented-update-groups](https://manual.gromacs.org/current/release-notes/2019/major/performance.html#implemented-update-groups) and [https://manual.gromacs.org/current/reference-manual/algorithms/parallelization-domain-decomp.html#coordinate-and-force-communication](https://manual.gromacs.org/current/reference-manual/algorithms/parallelization-domain-decomp.html#coordinate-and-force-communication) for more information. Regarding your simulation crashes, have you tried switching to the `c-rescale` barostat? That is often more stable than `Parinello-Rahman`. ---
**Author:** ![mannu](https://avatars.discourse-cdn.com/v4/letter/m/54ee81/32.png) [@mannu](https://gromacs.bioexcel.eu/u/mannu)\ **Post date:** [March 26, 2025, 5:56pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/3 "2025-03-26T17:56:25Z")
Dear Sir, Iam also getting similar notification in my output file. Iam you C -rescale barostat and not to sure where to start looking for these interdispersed atoms. Please guide me through this. Manisha ---
**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:** [March 27, 2025, 7:25am UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/4 "2025-03-27T07:25:12Z")
This is usually because a topology generation tool put all hydrogens at the end of groups instead of directly after the heavy atom they are connecte to. ---
**Author:** ![mannu](https://avatars.discourse-cdn.com/v4/letter/m/54ee81/32.png) [@mannu](https://gromacs.bioexcel.eu/u/mannu)\ **Post date:** [March 28, 2025, 2:48pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/5 "2025-03-28T14:48:28Z")
Ok Sir. So it is not an error or issue in the structure? It is not necessary to have that order ? ---
**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:** [April 1, 2025, 2:29pm UTC](https://gromacs.bioexcel.eu/t/update-groups-can-not-be-used-for-this-system-because-atoms-that-are-in-directly-constrained-togeth/9090/6 "2025-04-01T14:29:48Z")
This is only a performance, not a correctness issue.