unclear "dock" documentation

[camattelaer]

Hi all

not really a bug report, but i would like to clarify that the way of setting the level of theory for final optimizations in the documentation is unclear ( link to documentation ). More specifically this snippet:

I could not change the level of theory with either of these flags, so i had a look in the source and found that the correct way is by setting --optlvl <method> where <methid> is either gfn2, gfn1 or gfnff. (This is also defined in xtb dock --help)

I have two additional questions:

1. I could not find any way to turn off the fast flag. Is it even possible to do so?
2. Is there a way to monitor if dock is correctly applying e.g. the specified alpb or convergence criteria flag? since there is no individual output on optimizations, i can only monitor coordinates and respective energy/gnorm in final_opt.xyz. (Currently the --alpb flag is missing from the xtb dock --help but i did find a select-case for it in the dock.f90 source )

Thanks in advance!

Charles-Alexandre

[cplett]

Hi,
Thank you for the feedback.
Using the --gfnff, --gfn2, or --gfn1 flag should also work in addition to the --optlvl <method> flag. I will add the latter to the documentation for consistency.
The fast mode is turned off by default so you don't need to switch it off as long as you don't provide the --fast flag.
Currently, there isn’t a way to monitor whether setting the convergence criterion or solvation model was successful, but that's a great suggestion. I’ll consider adding it in future releases.

[camattelaer]

Hi
Thanks for the reply! I've been trying to reproduce the --gfnX problem, but unsuccesful so i am not sure what caused it but good to know that it should work.

On the fast flag: even if i call xtb without the flag, the output mentions that fast mode is selected (recommended) (see attached output example:
xtb_docking.txt