[gmx-users] 2016.3 only gmx grompp error on NVT step for ions

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 23 17:45:52 CET 2018


This is a new warning in that recent version of GROMACS, because we found
that constraints = all-bonds could produce artefacts. The error message
points out line 14 of your topology, which presumably relates to the QS21
molecule topology, not the ions. So it's probably triggered by one of the
aldehyde groups. As the message notes, the plausible fixes involve
reconsidering mdp options, not investigating in the topology. I'd first
consider not using all-bonds, and otherwise adjust the LINCS options


On Tue, Jan 23, 2018 at 5:21 PM Sarai G <saraigur2017 at gmail.com> wrote:

> Greetings and Salutations,
>>  1qs21-test_log
> <
> https://drive.google.com/file/d/1ZcrtdKW3TJnjIY9OpsyLG4P3zEFqkZLj/view?usp=drive_web
> >
> ​​
>  1qs21_nvt.mdp
> <
> https://drive.google.com/file/d/1x3Mb5OswZ5UH76nkB6CkrNAIBzHTPMLX/view?usp=drive_web
> >
> ​​
>  qs21_testNVT.mpg
> <
> https://drive.google.com/file/d/1SR9PvY-QC5y0myzJi4C8hC4o9ocPPuok/view?usp=drive_web
> >
> ​I was trying to create a reference system of water, some QS21, and K
> cations with all-bond constraints (which is a needed setting) only when I
> got the following error at the NVT step after energy minimization was
> successful;
> WARNING 1 [file Case5-1.top, line 14]:
>   There are atoms at both ends of an angle, connected by constraints and
>   with masses that differ by more than a factor of 13. This means that
>   there are likely dynamic modes that are only very weakly coupled. To
>   ensure good equipartitioning, you need to either not use constraints on
>   all bonds (but, if possible, only on bonds involving hydrogens) or use
>   integrator = sd or decrease one or more tolerances:
>   verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
>   4 or SHAKE tolerance <= 5e-06
> I tried many things to fix it including remaking the system and going
> through the force field files. Everything came out clean and the error only
> appeared in GROMACS 2016.3.I used -maxwarn 1 to test how the system looked
> in VMD, and the ion(s) were moving around fine. From what I have found,
> there appears to be no problem causing this error.
> Has anyone ran into the problem before?
> --
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