# Error compiling gromacs 2020.5 patched with Colvar module

**URL:** <https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048>\
**Category:** User discussions\
**Tags:** installation-error, colvars\
**Created:** [October 29, 2021, 1:01am UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048 "2021-10-29T01:01:43Z")\
**Posts on this page:** 5\
**Page:** 2

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**Author:** ![galileo92](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@galileo92](https://gromacs.bioexcel.eu/u/galileo92)\
**Post date:** [November 4, 2021, 12:14am UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048/21 "2021-11-04T00:14:40Z")

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Yes, Prof. Giacomo,

I’ve download gromacs 2020.6 patched with colvars, may question is is I can patch too it with plumed a same time?

Best,

Geo.

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**Author:** ![jhenin](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jhenin/32/1086_2.png) [@jhenin](https://gromacs.bioexcel.eu/u/jhenin)\
**Post date:** [November 4, 2021, 9:18am UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048/22 "2021-11-04T09:18:02Z")

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Hi Geo,

Yes, you can apply the Plumed patch the the Colvars-patched version. Just make sure that the patch applies cleanly - you will see warnings if it doesn’t (“hunk #… failed”).

Jérôme

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**Author:** ![galileo92](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@galileo92](https://gromacs.bioexcel.eu/u/galileo92)\
**Post date:** [November 4, 2021, 3:35pm UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048/23 "2021-11-04T15:35:03Z")

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Thanks so much Prof Jhenin!

Best,

Geo.

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**Author:** ![galileo92](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@galileo92](https://gromacs.bioexcel.eu/u/galileo92)\
**Post date:** [November 9, 2021, 11:26pm UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048/24 "2021-11-09T23:26:08Z")

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Dear Prof. Giacomo,

I’m pulling in the direction of Z, so I want to apply harmicWalls so that the protein confines in a certain radius, but I don’t really understand what values ​​to give to lowwall and upperwall

my protein has as COM in Z 6.4 nm and as maximum length in x and 6.2 nm, and my colvar is “distanceXY”

the radius could be 5.7 nm (0.5 nm less than the original length)

best,

Geo.

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**Author:** ![giacomo.fiorin](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/giacomo.fiorin/32/2862_2.png) [@giacomo.fiorin](https://gromacs.bioexcel.eu/u/giacomo.fiorin)\
**Post date:** [November 12, 2021, 6:31pm UTC](https://gromacs.bioexcel.eu/t/error-compiling-gromacs-2020-5-patched-with-colvar-module/3048/25 "2021-11-12T18:31:13Z")

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Hi, this last question is more dependent on your specific system. I can only clarify that distanceXY is always computed between two points, so if you want to restrain a group near a specific absolute position, you can make one of the two groups a dummyAtom. For GROMACS specifically, you would need to use the coordinates (Lx/2, Ly/2, Lz/2) to express the center of the box.

If you have further questions about Colvars that aren’t specific to GROMACS, those may go beyond this specific forum category. We’ll discuss between developers of both codes what would be the best place for this type of question.

To summarize this conversation: your initial compilation error with GCC 11 is unrelated to Colvars, and it is instead an issue of the _standard GROMACS 2020 release series_, which will eventually be addressed in a GROMACS patch release (probably 2020.7?).

Giacomo

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