[gmx-users] no domain decomposition

[Chetan Mahajan]

Thanks, Mark. I was translating a crystal and for some reason, C atom of
formate was getting displaced. Now, it's working.


On Wed, Jun 25, 2014 at 7:16 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Why do you have a bonded interaction whose length is 1.6nm? Mdrun is
> telling you that is limiting you.
>
> Mark
> On Jun 25, 2014 12:26 PM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
>
> > Hello,
> >
> > I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water)
> in
> > my system. I am getting following error:
> >
> >
> > Fatal error:
> > There is no domain decomposition for 16 nodes that is compatible with the
> > given box and a minimum cell size of 1.81239 nm
> > Change the number of nodes or mdrun option -rdd
> >
> >  Following is an excerpt of log file:
> >
> > Initializing Domain Decomposition on 16 nodes
> > Dynamic load balancing: no
> > Will sort the charge groups at every domain (re)decomposition
> > Initial maximum inter charge-group distances:
> >     two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163
> >   multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163
> > Minimum cell size due to bonded interactions: 1.812 nm
> > Using 0 separate PME nodes, as there are too few total
> >  nodes for efficient splitting
> > Optimizing the DD grid for 16 cells with a minimum initial size of 1.812
> nm
> > The maximum allowed number of cells is: X 1 Y 1 Z 6
> >
> >
> > *I tried decreasing number of nodes from 48 to 16, but this error appears
> > always. 2161 and 2163 atoms mentioned in log file excerpt above are
> formate
> > atoms each of which is in a different charge group. I can't put them in
> > same charge group, since they are different energy groups as we can see.
> *
> >
> > *Any suggestions how to interpret log file excerpt or what more can be
> > done?*
> >
> > Thanks
> > Chetan
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