Error compiling gromacs 2020.5 patched with Colvar module

User discussions
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21

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.

22

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

23

Thanks so much Prof Jhenin!

Best,

Geo.

24

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.

25

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