[gmx-users] the mdrun choked or maybe braked.

[Justin A. Lemkul]

#ZHAO LINA# wrote:
>  Hi,
> 
> The problem just like this, in md.log
> \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
> There are: 130889 Atoms
> splitting topology...
> Walking down the molecule graph to make constraint-blocks
> There are 43925 charge group borders and 43271 shake borders
> There are 43271 total borders
> Division over nodes in atoms:
>     9348    9348    9348    9351    9348    9351    9348    9351    
> 9348    9351
>     9348    9351    9348    9350
> Walking down the molecule graph to make constraint-blocks
> CPU=  0, lastcg= 3245, targetcg=25208, myshift=    8
> CPU=  1, lastcg= 6361, targetcg=28324, myshift=    8
> CPU=  2, lastcg= 9477, targetcg=31440, myshift=    8
> CPU=  3, lastcg=12594, targetcg=34557, myshift=    8
> CPU=  4, lastcg=15710, targetcg=37673, myshift=    8
> CPU=  5, lastcg=18827, targetcg=40790, myshift=    8
> CPU=  6, lastcg=21943, targetcg=43906, myshift=    7
> CPU=  7, lastcg=25060, targetcg= 3098, myshift=    7
> CPU=  8, lastcg=28176, targetcg= 6214, myshift=    7
> CPU=  9, lastcg=31293, targetcg= 9331, myshift=    7
> CPU= 10, lastcg=34409, targetcg=12447, myshift=    7
> CPU= 11, lastcg=37526, targetcg=15564, myshift=    7
> CPU= 12, lastcg=40642, targetcg=18680, myshift=    7
> CPU= 13, lastcg=43924, targetcg=21962, myshift=    8
> pd->shift =   8, pd->bshift=  0
> Division of bonded forces over processors
> CPU              0     1     2     3     4     5     6     7     8     
> 9    10 
>   11    12    13
> G96ANGLES     2376     0     0     0     0     0     0     0     0     
> 0     0 
>    0     0     0
> PDIHS          774     0     0     0     0     0     0     0     0     
> 0     0 
>    0     0     0
> IDIHS          852     0     0     0     0     0     0     0     0     
> 0     0 
>    0     0     0
> LJ14          2436     0     0     0     0     0     0     0     0     
> 0     0 
>    0     0     0
> CONSTR        1614     0     0     0     0     0     0     0     0     
> 0     0 
>    0     0     0
> SETTLE        2586  3116  3116  3117  3116  3117  3116  3117  3116  
> 3117  3116 
> 3117  3116  3034
> Workload division
> nnodes:          14
> pd->shift:        8
> pd->bshift:       0
> Nodeid   atom0   #atom     cg0       #cg
>      0       0    9348       0      3246
>      1    9348    9348    3246      3116
>      2   18696    9348    6362      3116
>      3   28044    9351    9478      3117
>      4   37395    9348   12595      3116
>      5   46743    9351   15711      3117
>      6   56094    9348   18828      3116
>      7   65442    9351   21944      3117
>      8   74793    9348   25061      3116
>      9   84141    9351   28177      3117
>     10   93492    9348   31294      3116
>     11  102840    9351   34410      3117
>     12  112191    9348   37527      3116
>     13  121539    9350   40643      3282
> 
> Max number of connections per atom is 27
> Total number of connections is 32076
> Max number of graph edges per atom is 4
> Total number of graph edges is 13572
> Initial temperature: 303.113 K
> 
> Started mdrun on node 0 Fri Aug 13 14:38:46 2010
> 
>            Step           Time         Lambda
>               0        0.00000        0.00000
> 
> Grid: 10 x 45 x 10 cells
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     2.96784e+03    1.16372e+03    9.89996e+02   -1.07478e+01    2.63019e+04
>         LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
>     3.11913e+05   -8.40005e+03   -2.19295e+06   -1.39523e+04   -3.36479e+04
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>    -1.90563e+06    3.31599e+05   -1.57403e+06    3.04444e+02    1.07070e+01
>   Cons. rmsd ()
>     2.63140e-05
> \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
> 
> Nothing more at the end,
> I changed the 16 cores to 14 cores, still has the same problem. And when 
> I checked the status, it showed me it's finished.
> 

Please provide more information.  It mdrun stopped, it must have had a reason. 
Please provide your .mdp file, description of the system, and what you did as 
far as energy minimization and/or equilibration prior to whatever this run was 
doing.  If mdrun fails, there's always a reason, and it would be very odd if 
Gromacs simply stopped without providing some kind of indicative output.

-Justin

> Thanks for any advice,
> 
> lina
> 
> 

-- 
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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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