[gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 117

[Sarai G]

​Hello,

Line 14 relates to the ions, not the QS21. In all runs and testing, the
error was always relating to the ions. Different systems both with and
without ions were created using QS21 and other molecules and the error only
appeared when there were ions involved. Ensuring that the reference line
was in fact the ions and not the QS21 was the first thing I did.

Sarai​

Date: Tue, 23 Jan 2018 16:45:38 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: "gromacs.org_gm." <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] 2016.3 only gmx grompp error on NVT step for
>         ions
> Message-ID:
>         <CAMNuMASbi=-Phczuq-gY=FDnL30yyFs3K0tFDBZsUwviLxAH5A at mail.gm
> ail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> 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
>
> Mark
>
> 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/1ZcrtdKW3TJnjIY9OpsyLG4P3zEF
> qkZLj/view?usp=drive_web
> > >
> > ??
> >  1qs21_nvt.mdp
> > <
> > https://drive.google.com/file/d/1x3Mb5OswZ5UH76nkB6CkrNAIBzH
> TPMLX/view?usp=drive_web
> > >
> > ??
> >  qs21_testNVT.mpg
> > <
> > https://drive.google.com/file/d/1SR9PvY-QC5y0myzJi4C8hC4o9oc
> PPuok/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?
> >
> >
> > --
> > *I fancy days of yore, quote the Raven nevermore.*
> > --
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>
>


-- 
*I fancy days of yore, quote the Raven nevermore.*