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

[Chang Woon Jang]

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
-------------------------------------------------------


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
>
> * Please search the archive at http://www.gromacs.org/Support
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