[gmx-users] decomposition error

[Justin Lemkul]

On 7/22/16 7:03 PM, Chang Woon Jang wrote:
> Dear Justin A. Lumkul,
>
>    Thank you for your answer. I am sorry for asking what is DD. My topology
> topol.top file is below. Would you please tell me about what is DD? How can
> I set up in topology file?
>

DD = domain decomposition.  Please look in the .log file for how it is being set 
up and provide that information if you need help troubleshooting it.  Also use 
Google; this error comes up (and gets solved) every couple of days.

-Justin

> Thank you.
>
> Best regards,
> Changwoon Jang
>
>
>
> [ defaults ]
>
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>
>   1             1               no              0.0     0.0
>
>
> [ atomtypes ]
>
> ;type    mass    charge       ptype          sigma      epsilon
>
>  A     75.087799  0.000       A        1.000000000  1.000000000
>
>  B     76.097998  0.000       A        1.000000000  1.000000000
>
>  C     42.080999  0.000       A        1.000000000  1.000000000
>
>  D     74.103099  0.000       A        1.000000000  1.000000000
>
>  E     99.153398 0.000       A        1.000000000  1.000000000
>
>  F     116.160799  0.000       A        1.000000000  1.000000000
>
>  G     58.080399 0.000       A        1.000000000  1.000000000
>
>
> [ moleculetype ]
>
> DGA 3
>
>
> [atoms]
>
> ; nr type resnr residue atom cgnr charge mass
>
> 1 A 1 DGA A1 1 0.000000 75.087799
>
> 2 B 1 DGA B1 2 0.000000 76.097998
>
> 3 C 1 DGA C 3 0.000000 42.080999
>
> 4 B 1 DGA B2 4 0.000000 76.097998
>
> 5 A 1 DGA A2 5 0.000000 75.087799
>
>
>
> [ bonds ]
>
> 1 2  8 1  1.0 ; 1:bond:1
>
> 2 3  8 1  1.0 ; 1:bond:2
>
> 3 4  8 1  1.0 ; 1:bond:3
>
> 4 5  8 1  1.0 ; 1:bond:4
>
>
> [ angles ]
>
> 1 2 3  8 1 1.0 ; 1:angle:1
>
> 2 3 4  8 1 1.0 ; 1:angle:2
>
> 3 4 5  8 1 1.0 ; 1:angle:3
>
>
> [ dihedrals ]
>
> 1 2 3 4  8 1 1.0 ; 1:ABCBdihedral:1
>
> 2 3 4 5  8 1 1.0 ; 1:ABCBdihedral:2
>
>
> [ moleculetype ]
>
> J400 3
>
>
> [atoms]
>
> ; nr type resnr residue atom cgnr charge mass
>
> 1 D 1 J400 D1 1 0.000000 74.103099
>
> 2 E 1 J400 E1 2 0.000000 99.153398
>
> 3 F 1 J400 F1 3 0.000000 116.160799
>
> 4 G 1 J400 G1 4 0.000000 58.080399
>
> 5 D 1 J400 D2 5 0.000000 74.103099
>
>
> [ bonds ]
>
> 1 2  8 1 1.0 ; 1:bond:1
>
> 2 3  8 1 1.0 ; 1:bond:2
>
> 3 4  8 1 1.0 ; 1:bond:3
>
> 4 5  8 1 1.0 ; 1:bond:4
>
>
> [ angles ]
>
> 1 2 3  8 1 1.0 ; 1:angle:1
>
> 2 3 4  8 1 1.0 ; 1:angle:2
>
> 3 4 5  8 1 1.0 ; 1:angle:3
>
>
> [ dihedrals ]
>
> 1 2 3 4   8 1 1.0 ; 1:dihedral:1
>
> 2 3 4 5   8 1 1.0 ; 1:dihedral:2
>
>
> [ system ]
>
> ; Name
>
> Built with Packmol
>
>
> [ molecules ]
>
> ; Compound        #mols
>
> DGA       200
>
> J400       100
>
>
> On Fri, Jul 22, 2016 at 6:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/22/16 6:50 PM, Chang Woon Jang wrote:
>>
>>> Dear Grimaces Users,
>>>
>>> I have the decomposition error. I have tried to reduce the number of cores
>>> but still have the same problem. In my conf.gro, the cell size is about
>>> 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm.
>>>
>>>  Would you please give me some comments or relevant topics addressed?
>>>
>>>
>> The .log file tells you how DD is being set up and what the the limiting
>> interactions are.  Verify that your topology is sound from what the .log
>> tells you.
>>
>> -------------------------------------------------------
>>>
>>> Program gmx, VERSION 5.0.7-dev-20151003-1909f2f
>>>
>>> Source code file:
>>> /home1/02271/huddack/votca_install/src/gromacs/src/gromacs/mdlib/domdec.c,
>>> line: 6902
>>>
>>>
>> Also make sure your run isn't failing because of something due to hacked
>> code. Development versions generally shouldn't be used for production-level
>> science.
>>
>> -Justin
>>
>>
>>> Fatal error:
>>>
>>> There is no domain decomposition for 16 ranks that is compatible with the
>>> given box and a minimum cell size of 1.875 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
>>>
>>> -------------------------------------------------------
>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
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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

==================================================