[gmx-users] Mdrun with rdd option

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 23 10:31:43 CET 2016


On Tue, Feb 23, 2016 at 6:25 AM Raju Lunkad <
r.lunkad at students.iiserpune.ac.in> wrote:

> Dear Gromacs users,
> I am trying to run a simulation but I am getting the error regarding the
> domain decomposition.

Which error? People often can't help much without precise information.
Probably your system is unstable and was
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and your
"solution" below is just hiding the real problem.

I ran the simulation using "rdd" option and it is
> running fine.
> Kindly tell me whether "-rdd" option will affect my simulation. If yes,
> then which values would get affected using "rdd"  option.

mdrun has to choose a minimum diameter for the domains in the decomposition
for various code to work well. Choosing rdd too small risks that diameter
being too small, which means that the simulation might abort if the domain
becomes too small for all the atoms in a bonded interaction to be present
in one domain (see brief description at gmx mdrun -h). But in practice
almost nobody should have any need to change these things.


> Best Regards,
> Raju Lunkad
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