[gmx-users] Domain decomposition problems

Olivia Waring owaring at princeton.edu
Fri Feb 24 18:52:57 CET 2012

Dear Gromacs users,

Could someone please shed light on the following problem? My system
consists of an alkanethiol SAM (in the xy plane) with a layer of water on
top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5,
but the SAM flies apart and the simulation crashes. I'm trying to lengthen
the box in the z direction (and of course, resolvating the system) to see
if that solves the problem. Unfortunately, this seems to give rise to
domain decomposition issues... I get the following output in my md.log file:

Initial maximum inter charge-group distances:
    two-body bonded interactions: 0.424 nm, LJ-14, atoms 36 39
  multi-body bonded interactions: 0.424 nm, Ryckaert-Bell., atoms 36 39
Minimum cell size due to bonded interactions: 0.467 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.794 nm
Estimated maximum distance required for P-LINCS: 0.794 nm
This distance will limit the DD cell size, you can override this with -rcon
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 6 cells with a minimum initial size of 0.992 nm
The maximum allowed number of cells is: X 1 Y 1 Z 5
Fatal error:
There is no domain decomposition for 6 nodes that is compatible with the
given box and a minimum cell size of 0.9925 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS

I've experimented a bit with -rcon and with the number of nodes, but I
really have no idea what I'm doing! Any thoughts would be appreciated.
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