# The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance **URL:** \ **Category:** User discussions\ **Tags:** grompp\ **Created:** [May 11, 2022, 3:12pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153 "2022-05-11T15:12:43Z")\ **Posts on this page:** 18\ **Page:** 1
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 11, 2022, 3:12pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/1 "2022-05-11T15:12:43Z")
GROMACS version: 2022.1 GROMACS modification: No When using editconf to make a box from a crystal lattice (4x4x4 unit cells) and using a gro file which is fine, I get a new gro file where there are some bad H-H interactions. Moreover, when I try to run grompp in order to do an energy minimization, I get the error: The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance. This will lead to missing long-range corrections in the forces and energies. I have never encountered this error before and I am wondering what has caused it. I am using a cut-off distance of 1.0 which I can’t increase without also increasing the box, but I don’t think that this is the problem. Any help would be appreciated, Thanks, Peter ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [May 11, 2022, 6:07pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/2 "2022-05-11T18:07:41Z")
Hello Peter! That’s a new check that was introduced in GROMACS 2022, see [Miscellaneous — GROMACS 2022 documentation](https://manual.gromacs.org/2022/release-notes/2022/major/miscellaneous.html#grompp-now-warns-when-exclusion-forces-might-be-missing). It is there to prevent you from getting mildly incorrect energies, but I suppose that’s not a concern if you only want to do minimization. As a workaround now, you can use an older version of GROMACS to run `grompp`. But, if you want to run proper MD later, make sure the error does not appear with minimized structure. We will probably add a way to circumvent this warning in the future releases of GROMACS. ---
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 11, 2022, 7:18pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/3 "2022-05-11T19:18:10Z")
OK. I’ll try what you suggested. T Thanks, Peter ---
**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:** [May 12, 2022, 7:52am UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/4 "2022-05-12T07:52:59Z")
Could it be that molecules are broken over PBC in the structure you used for stacking? ---
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 13, 2022, 11:32am UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/5 "2022-05-13T11:32:07Z")
First of all, I followed Andrey’s suggestion which solved the problem. I only had to use a previous version of grompp once and after I succeeded to minimize the structure the errors no longer appeared in the equilibration and production phases. As to Berk’s question, I looked at the gro file generated by editconf upon making the box in PyMol and I didn’t see any broken molecules. Moreover, I was under the impression that broken molecules aren’t a problem for Gromacs and that they just affect the visualization of the system. Thanks again for your help. ---
**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:** [May 13, 2022, 12:51pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/6 "2022-05-13T12:51:55Z")
If Andrey’s suggestion solved your issue, then we should probably allow such distances during minimization. ---
**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:** [May 13, 2022, 12:58pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/7 "2022-05-13T12:58:29Z")
But you can use -maxwarn 1 and then grompp should also work with GROMACS 2022, right? We could consider changing this to a note when doing energy minimization. ---
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 13, 2022, 2:36pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/8 "2022-05-13T14:36:34Z")
I agree. ---
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 13, 2022, 2:37pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/9 "2022-05-13T14:37:52Z")
No. That’s the problem. It’s an “error” and not a “warning.” ---
**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:** [May 13, 2022, 3:29pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/10 "2022-05-13T15:29:22Z")
I uploaded a change to the release-2022 to change this to a warning. ---
**Author:** ![PSS67](https://avatars.discourse-cdn.com/v4/letter/p/ee59a6/32.png) [@PSS67](https://gromacs.bioexcel.eu/u/PSS67)\ **Post date:** [May 13, 2022, 7:47pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/11 "2022-05-13T19:47:47Z")
Thank you. ---
**Author:** ![nickytenner](https://avatars.discourse-cdn.com/v4/letter/n/bbce88/32.png) [@nickytenner](https://gromacs.bioexcel.eu/u/nickytenner)\ **Post date:** [October 16, 2022, 7:52am UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/12 "2022-10-16T07:52:16Z")
Hello, What I did was I increased the cut-off and minimized the structure. After that I reduced the cut-off and proceeded with MD. Nicky ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 25, 2025, 8:42pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/14 "2025-01-25T20:42:43Z")
@hess I am using parameters for PEG molecules developed by another group, originally validated with GROMACS 2021. However, when using these parameters in GROMACS 2022 for my current study, I encountered the following error, which did not occur in the 2021 version: The largest distance between excluded atoms is 1.775 nm ERROR 1 [file run.mdp]: The largest distance between excluded atoms is 1.775 nm, which is larger than the cut-off distance. This will lead to missing long-range corrections in the forces and energies. Could you please advise on how to resolve this error in GROMACS 2022? Since I am unable to modify the parameters, I am looking for potential adjustments or solutions compatible with this newer version. Thank you. ---
**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:** [January 26, 2025, 8:19pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/15 "2025-01-26T20:19:14Z")
Which GROMACS 2022 patch release are you using? The error was changed to a warning in 2022.2. Does this thread help at all, [Excluded distance larger than cutoff in ligand with virtual site](https://gromacs.bioexcel.eu/t/excluded-distance-larger-than-cutoff-in-ligand-with-virtual-site/9783)? ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 27, 2025, 11:34am UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/16 "2025-01-27T11:34:34Z")
Hi, It’s Gromacs 2022.0. I will go through the thread. May I know whether you suggest changing the GROMACS version to avoid the error message? ---
**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:** [January 27, 2025, 11:59am UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/17 "2025-01-27T11:59:15Z")
I advice you to always use the latest patch release of the main version you are using. There might be bugs that get fixed. If you can switch to the latest main release, that’s of course even better. ---
**Author:** ![Ema2022](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Post date:** [January 28, 2025, 7:23pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/18 "2025-01-28T19:23:11Z")
Noted. Thank you very much for your valuable comments. ---
**Author:** ![tonmoy](https://avatars.discourse-cdn.com/v4/letter/t/e36b37/32.png) [@tonmoy](https://gromacs.bioexcel.eu/u/tonmoy)\ **Post date:** [February 5, 2025, 3:12pm UTC](https://gromacs.bioexcel.eu/t/the-largest-distance-between-excluded-atoms-is-1-725-nm-which-is-larger-than-the-cut-off-distance/4153/19 "2025-02-05T15:12:48Z")
Faced the same issue, your suggestion helped. The molecules were broken at the boundaries.