# Standard library logic error

**URL:** <https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [December 23, 2022, 7:10pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475 "2022-12-23T19:10:47Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Narges](https://avatars.discourse-cdn.com/v4/letter/n/7993a0/32.png) [@Narges](https://gromacs.bioexcel.eu/u/Narges)\
**Post date:** [December 23, 2022, 7:10pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/1 "2022-12-23T19:10:47Z")

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GROMACS version: 2022.3  
GROMACS modification: Yes/No  
Hi all,

While using gmx msd I was faced with the error:

Standard library logic error (bug):  
(exception type: St12length\_error)  
vector::\_M\_default\_append

Does anybody know what it is for?

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**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:** [December 24, 2022, 12:51pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/2 "2022-12-24T12:51:47Z")

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Hi!

That’s an internal error in GROMACS. Could you please share the input file and the command you used?

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**Author:** ![Narges](https://avatars.discourse-cdn.com/v4/letter/n/7993a0/32.png) [@Narges](https://gromacs.bioexcel.eu/u/Narges)\
**Post date:** [December 24, 2022, 2:25pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/3 "2022-12-24T14:25:25Z")

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I want to calculate the diffusion coefficient of methane in polymer using:

gmx msd -f NPT.trr -s NPT.tpr -o MSD.xvg

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**Author:** ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer)\
**Post date:** [December 25, 2022, 11:16am UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/4 "2022-12-25T11:16:22Z")

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Hello,

to continue from what Andrey said, can you please open a bug for this on Gitlab ([Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues)) and attach the inputs (or another sample) that cause the bug?

Thanks!

Paul

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**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:** [December 28, 2022, 1:11pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/5 "2022-12-28T13:11:26Z")

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Nothing wrong with the command, but, as Paul said, we need the input file to diagnose the problem. You can attach it here; no strict need to go to GitLab (it will make things slightly easier for us, but the difference is minimal).

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**Author:** ![Narges](https://avatars.discourse-cdn.com/v4/letter/n/7993a0/32.png) [@Narges](https://gromacs.bioexcel.eu/u/Narges)\
**Post date:** [December 29, 2022, 4:42pm UTC](https://gromacs.bioexcel.eu/t/standard-library-logic-error/5475/6 "2022-12-29T16:42:35Z")

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thank you pbauer. I did it.