[gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Yes.. I used VMD for conversion...

On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Hi
>
> Sounds strange to my little knowledge. How I would justify is, it may be
> due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not
> sure.
>
> So you have converted the file format using VMD?
>
>
>
> On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer <sah2714 at gmail.com>
> wrote:
>
> > Hi,
> >
> > Thanks for the reply. I am only doing a rerun of a trajectory that has
> > already evolved without any dynamic load balancing problems.
> > -rerun only recalculates energies right. I don't understand why the same
> > trajectory is giving decomposition error now.
> >
> > On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Hi.
> > >
> > > That indicates a  problem with dynamic load balancing. Try to build
> > > different sizes of the box.
> > >
> > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer <sah2714 at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I am trying to calculate interaction between specific residues using
> > gmx
> > > > mdrun -rerun flag. The trajectory was in a dcd format, which I
> > converted
> > > to
> > > > a trr file. I get the following error -
> > > >
> > > > Domain decomposition has not been implemented for box vectors that
> have
> > > > non-zero components in directions that do not use domain
> decomposition:
> > > > ncells
> > > > = 1 8 1, box vector[2] = 0.000000 10.536000 0.000000
> > > >
> > > > Can someone please tell me what could be going wrong here ?
> > > > --
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> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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