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

[Justin Lemkul]

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
>>>
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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

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