[gmx-users] Domain decomposition error with -rerun

Mark Abraham mark.j.abraham at gmail.com
Sat Apr 28 13:02:29 CEST 2018


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 ?
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list