[gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Thanks for the reply Mark.

On Sat, Apr 28, 2018 at 4:32 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Clearly the conversion tool did not produce a file that conforms to the
> requirements GROMACS has for specifying periodic boxes. That may not work
> well even if you'd run mdrun without domain decomposition because the
> periodicity may not be understood correctly. Find out what was going on and
> how the conversion may have worked.
>
> Mark
>
> On Sat, Apr 28, 2018, 09:54 Sahithya S Iyer <sah2714 at gmail.com> wrote:
>
> > 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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