[gmx-users] decomposition error

[Chang Woon Jang]

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?

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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