Tomy van Batis wrote:
Dear all
The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I
experience some difficulties when running in parallel.
Initially, my simulation box has dimensions :
* 3.30507 2.67145 41.15800*
and it consists of 25 polymers chains with 50 beads/chain
When I run NVT using 8 or 16 cores, everything is working fine, but when
I compress it to dimensions:
*3.30507 2.67145 10.64441*
and try again to run NVT in 8 cores, I have the following error message:
/There is no domain decomposition for 8 nodes that is compatible with
the given box and a minimum cell size of 2.5 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings/
As I saw this is well known error, but I can't understand how to fix it :-)
A nearly identical case was posted just a few days ago, and reasons for the
error discussed:
http://lists.gromacs.org/pipermail/gmx-users/2011-March/059063.html
with a possible work-around:
http://lists.gromacs.org/pipermail/gmx-users/2011-March/059079.html
From what I understood, this is happening because_* I use constrains in
all the bonds of my system*_
Constraints are but one of many considerations in establishing DD cells.
-Justin
In my .log file I see the following:
/Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 0.000 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm
Estimated maximum distance required for P-LINCS: 2.000 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 8 cells with a minimum initial size of 2.500 nm
The maximum allowed number of cells is: X 1 Y 1 Z 4/
, but I can't understand how to use -rcon or -dds in order to fix my problem
Any suggestions?
Thanks in advance
Chrysostomos
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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