On 25/02/2012 4:52 AM, Olivia Waring wrote:
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
settings
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.
A given implementation cannot run an arbitrary simulation system
efficiently in parallel on an arbitrary number of processors. The
GROMACS implementation needs to be able to localize a chunk of nearby
atoms to the same processor in a 3D grid of processors. Your system is
too small for it to find a satisfactory chunk for each processor. Use
more atoms or fewer processors. A very rough guideline is to use at
least about 1000 atoms per processor - but the real constraints are
geometric.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
