[gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box

[Seyed Mojtaba Rezaei Sani]

Dear Justin

Thanks for your kind response. I didn't notice the point you mentioned. It
seems that grompp doesn't care the difference betwen vdwq and vdw-q.
however, I corrected the script. The error remains even in the case of
choosing 2 nodes. The only way to have a successful run is a serial
calculation. I attach the md.log file to this message. I would appreciate
any help you could provide.

On Tue, May 5, 2015 at 5:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/5/15 8:48 AM, Seyed Mojtaba Rezaei Sani wrote:
>
>> Dear gmx users,
>>
>> Perhaps my problem is a repetitive question in the forum but I couldn't
>> find a trouble-shooter response for my case.
>> I am running a stochastic dynamics calculation for a solution of
>> doxorubicin. The following error occurs while the calculation runs:
>>
>> Fatal error:
>> There is no domain decomposition for x nodes that is compatible with the
>> given box and a minimum cell size of 1.9433 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>>
>> I have tried several numbers of nodes resulting in the same error. Here is
>> the mdp file:
>>
>> integrator               = sd
>> nsteps                   = 1000000
>> dt                       = 0.002
>> nstenergy                = 1000
>> nstlog                   = 5000
>> ; turn off trajectory writing
>> nstxout                  = 0
>> nstvout                  = 0
>> ; cut-offs at 1nm
>> rlist                    = 1.0
>> nstlist                  = 10
>> coulombtype              = pme
>> vdw-type                 = cut-off
>> rvdw                     = 1.0
>> constraints              = all-bonds
>> ; set temperature to 300K
>> tcoupl                   = v-rescale
>> tc-grps                  = system
>> tau-t                    = 0.2
>> ref-t                    = 300
>> ; and pressure to 1 bar
>> pcoupl                   = parrinello-rahman
>> ref-p                    = 1
>> compressibility          = 4.5e-5
>> tau-p                    = 5
>> ; and set the free energy parameters
>> free-energy              = yes
>> couple-moltype           = DOX
>> init-lambda              = 0
>> ; these 'soft-core' parameters make sure we never get overlapping
>> ; charges as lambda goes to 0
>> sc-power                 = 1
>> sc-sigma                 = 0.3
>> sc-alpha                 = 1.0
>> ; we still want the molecule to interact with itself at lambda=0
>> couple-intramol          = no
>>
>
> This is what triggers the error.  Note from the manual, for
> couple-intramol = no:
>
> "All intra-molecular non-bonded interactions for moleculetype
> couple-moltype are replaced by exclusions and explicit pair interactions.
> In this manner the decoupled state of the molecule corresponds to the
> proper vacuum state without periodicity effects."
>
> The added exclusions and pairs require larger DD cells to be constructed
> because these bonded interactions occur over larger distances than normal.
> This limits the size of the DD cells and hence how many processors/cores
> you can use.  You haven't said how many you're trying to use, but the
> solution is simply to use fewer.
>
>  couple-lambda1           = vdwq
>>
>
> The option is "vdw-q" but I don't know if grompp magically translates it.
> Just check.
>
> -Justin
>
> --
> ==================================================
>
> 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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-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)