#ZHAO LINA# wrote:
Hi,
The problem just like this, in md.log
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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
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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
--
========================================
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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