[gmx-users] domain decomposition errors

[pedro alberto valiente flores]

Thanks david:
the chrash error is :
Making 2D domain decomposition 4 x 2 x 1
starting mdrun 'PLASMEPSIN 2 in water'
30000000 steps,  60000.0 ps.

Step 33, time 0.066 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.084460, max 31.492893 (between atoms 3168 and 3169)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3166   3168  113.4    0.1330   0.3588      0.1330
   3166   3167   30.3    0.1230   0.1460      0.1230
   3168   3170  120.4    0.1470   0.5973      0.1470
   3168   3169   95.2    0.1000   3.2493      0.1000
   3170   3175   90.3    0.1530   0.3208      0.1530
   3170   3171  113.9    0.1530   0.5267      0.1530
   3171   3174  118.6    0.1530   0.5368      0.1530
   3171   3172  126.1    0.1430   0.7276      0.1430
   3172   3173  133.3    0.1000   0.4373      0.1000
   3175   3177   48.2    0.1330   0.1956      0.1330
   3175   3176   45.2    0.1230   0.1736      0.1230
Warning: 1-4 interaction between 3153 and 3169 at distance 3.484 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

David, briefly you can explain me which is de difference between 
-dd 4 2 1 and -dd 2 2 2 how I can suitable set this parameter?
sincerely my best regards,
pedro
On Thu, 2009-11-26 at 21:10 +0100, David van der Spoel wrote:
> pedro alberto valiente flores wrote:
> > Hi gromacs users:
> > I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic
> > box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation
> > crashes. In attach are files.tgz which contains the log 
> > (PlmII+PepstatinA_free.log) and error files (BSA.err.%j). However, I can
> > run the simulation without problems in 2 processors (PlmII
> > +PepstatinA_equilibration.log). Can I fix this error setting domain
> > decomposition parameters of mdrun. I going to appreciate any
> > suggestions,
> >   
> Have you played with the -dd flag?
> E.g. -dd 2 2 2?
> 
> Please don't attach files but describe your problem concise but clear.
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
-- 
MC Pedro Alberto Valiente Flores
Centro de Estudios de Proteínas
Facultad de Biología
Universidad de La Habana