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

[Mark Abraham]

On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani <
s.m.rezaeisani at gmail.com> wrote:

> 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.


Then that's life (except that if your protein is non-spheroidal, you might
have better luck with the long axis aligned to the z-axis).

The domain decomposition code expects bonded interactions to be of shorter
range than short-ranged non-bonded interactions, so will not produce a
decomposition that has a bonded interaction that starts in one domain,
crosses another domain, leaves by the opposite face, and reaches a third
domain. This is implemented by setting a minimum size for domains based on
many properties of the observed starting structure. There's a brief summary
of these choices printed in every .log file.

The use of couple-intramol triggers the generation of atypical
interactions, that are implemented like bonds as far as the DD code knows,
and for a protein those "bonds" are so much longer that they set a minimum
size that means a decomposition is infeasible.

AFAIK, FEP on a whole protein isn't going to work at all anyway.

Mark

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)
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