[gmx-users] The maxwarn fatal errors

[Justin Lemkul]

On 1/6/20 9:40 PM, 변진영 wrote:
> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling. During tutorial, When I treid to input the command line:
>    gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>    Fatal error:
>    Too many warnings (2).
>     If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>   WARNING 1 [file topol.top, line 56]:
>    The GROMOS force fields have been parametrized with a physically
>    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>    used with a single-range cut-off (or a correct Trotter
>    multiple-time-stepping scheme), physical properties, such as the density,
>    might differ from the intended values. Since there are researchers
>    actively working on validating GROMOS with modern integrators we have not
>    yet removed the GROMOS force fields, but you should be aware of these
>    issues and check if molecules in your system are affected before
>    proceeding. Further information is available at
>    https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
>    decision to remove physically incorrect algorithms can be found at
>    https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>    With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>    should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this problem?

The first warning is very verbose and provides you with substantial 
justification and background reading.

As for the second, change tau-p to 2 as suggested. Note that I have not 
made any attempt to update the tutorials for the 2020 version, and they 
are only guaranteed to be compatible with GROMACS 2018.x versions.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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