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

Tue Jan 23 18:21:31 CET 2018

Hello Justin,

Sorry about the subject line, I fixed it this time around.

I have the .itp files (toppar folder) and the .top files as you requested
as well as a larger tar.gz which all of the files produced in the testing
run within it.

Sarai

> Date: Tue, 23 Jan 2018 12:04:08 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue
>         117
> Message-ID: <952be550-0f76-72a9-90df-5e846727d810 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/23/18 12:02 PM, Sarai G wrote:
> > ?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.

 Then something is problematic in your topology. Please upload the .top
 and .itp files if you want further commentary on it.

 -Justin
>
> > 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.*
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
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> >>
> >>
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================

 1qs21.top
<https://drive.google.com/file/d/1tHlkY-TMlLTtn89Wi9HEq52PiJ-llwwN/view?usp=drive_web>

 toppar.tar.gz
<https://drive.google.com/file/d/1aTJXUUhsYX0jhbOL5b_DXwpR57XqfATd/view?usp=drive_web>

 QS21-Testing.tar.gz
<https://drive.google.com/file/d/1BPtA7-z4Ye-pLBsTDd-E5_xqWuP5nLl3/view?usp=drive_web>

 1qs21_nvt.mdp
<https://drive.google.com/file/d/1x3Mb5OswZ5UH76nkB6CkrNAIBzHTPMLX/view?usp=drive_web>

 1qs21-test_log
<https://drive.google.com/file/d/1ZcrtdKW3TJnjIY9OpsyLG4P3zEFqkZLj/view?usp=drive_web>

I fancy days of yore, quote the Raven nevermore.