[gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Tue Aug 30 18:06:18 CEST 2016

Dear Justin,

     Search engine give a clue about using -nt options. However, how to
choose the proper number for -nt option from the error message?

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 12:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/30/16 11:52 AM, Chang Woon Jang wrote:
>
>> Dear Justin Lemkul,
>>
>>     Thank you for your answers. The following is the error message after I
>> run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
>> 2.5".
>>
>>
>> Initializing Domain Decomposition on 8 ranks
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Minimum cell size due to bonded interactions: 2.500 nm
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm
>> The maximum allowed number of cells is: X 1 Y 1 Z 1
>>
>> -------------------------------------------------------
>> Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
>> Source code file:
>> /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line:
>> 6902
>>
>> Fatal error:
>> There is no domain decomposition for 8 ranks that is compatible with the
>> given box and a minimum cell size of 3.125 nm
>> Change the number of ranks or mdrun option -rdd or -dds
>> Look in the log file for details on the domain decomposition
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>>
> And what does Google tell you about this particular case?  Hint: the same
> error gets posted to this list pretty much weekly, if not more often.  It's
> been rationalized and solved time and time again.
>
> -Justin
>
>
>
>> Best regards,
>> Changwoon Jang
>>
>>
>> On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 8/30/16 10:41 AM, Chang Woon Jang wrote:
>>>
>>> Dear Justin Lemkul,
>>>>     Thank you for your response. Yes, I use coarse-grained system
>>>> (thermosetting polymer). I prepared the system from the equilibrated
>>>> atomistic system. The atomistic system was equilibrated using OPLS-AA
>>>> force
>>>> filed under NPT and NVT for almost 40 ns. The initial atomistic system
>>>> contained 13854 atoms. The equilibrated atomistic system was
>>>> coarese-grained (mapped) with certain criteria. Now, I am trying to get
>>>> CG
>>>> potentials using iterative Boltzmann Inversion, but this error keeps me
>>>> dizzy.
>>>>
>>>>     Whenever I use -rdd options, it gives another error like domain
>>>> decomposition error with other options recommended. Whenever I use -nt
>>>>
>>>>
>>> Please always post exact error messages, copied and pasted directly from
>>> the terminal or .log file.  We can't guess at what you're reading.
>>>
>>> options, the simulation goes well but the simulation trajectory seem
>>> weird
>>>
>>>> that some molecules are going out the simulation box
>>>>
>>>>
>>>> This is just PBC.  There is no "outside" of a box.  If you've got
>>> polymers, they will elongate and contract depending on their physical
>>> behavior.  There's nothing wrong with that.
>>>
>>> -Justin
>>>
>>>
>>>     It seems tricky to find what is the problem.
>>>
>>>>
>>>> Thank you.
>>>>
>>>> Best regards,
>>>> Changwoon Jang
>>>>
>>>> On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 8/29/16 6:02 PM, Chang Woon Jang wrote:
>>>>>
>>>>> Dear Gromacs Users,
>>>>>
>>>>>>
>>>>>>
>>>>>> I have a Fatal error as follow. The error says -rdd option or
>>>>>> -ddcheck.
>>>>>> How
>>>>>> can I properly use these options? Is the following command the proper
>>>>>> use
>>>>>> of these options?
>>>>>>
>>>>>> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5
>>>>>>
>>>>>>
>>>>>>> -ddcheck
>>>>>>>
>>>>>>
>>>>>>
>>>>>> Yes, but note that -ddcheck is on by default anyway, and you should
>>>>>> look
>>>>>>
>>>>> into why this might be happening.  You can get around this error, but
>>>>> it
>>>>> often indicates instability.  Without a complete description of what
>>>>> your
>>>>> system is, what you've previously done to prepare, minimize,
>>>>> equilibrate,
>>>>> etc. we're sort of just guessing here.  If the system is coarse grain,
>>>>> then
>>>>> use of a large -rdd is typical (as you will see from many threads in
>>>>> the
>>>>> archive that address this case specifically).
>>>>>
>>>>> -Justin
>>>>>
>>>>> Thank you.
>>>>>
>>>>>
>>>>>>
>>>>>> 1 of the 1612 bonded interactions could not be calculated because some
>>>>>> atoms involved moved further apart than the multi-body cut-off
>>>>>> distance
>>>>>> (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd,
>>>>>> for
>>>>>> pairs and tabulated bonds also see option -ddcheck
>>>>>> For more information and tips for troubleshooting, please check the
>>>>>> GROMACS
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Best regards,
>>>>>> Changwoon Jang,
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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