[gmx-users] error:Segmentation fault

[郭建路]

Hello everyone
I am doing MD on a protein, and everything including the EM seems to go well. When I start to do the position restrained MD (or even directly the MD without doing the PR MD), I get a "Segmentation fault". 

when a doing EM,I set  nsteps = 500,because i just want to go though the  procedures,but there is a result:

Steepest Descents did not converge to Fmax < 1000 in 501 steps.

 i go on the grompp pr.mdp and mdrun command, Segmentation fault comes up.details as followed:

Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.060225 (between atoms 4110 and 4112) rms 0.001990
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'CYP2W1_CYSHEME in water'
100 steps,      0.2 ps.


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 20.941092 (between atoms 4012 and 4013) rms 0.630786
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4008   4010   59.8    0.1470   0.2246      0.1470
   4010   4011   87.3    0.1536   1.1098      0.1530
   4010   4023   56.2    0.1530   0.2198      0.1530

........

........ so much atoms number
  Warning: 1-4 interaction between 4008 and 4012 at distance 1.404 which is larger than the 1-4 table size 1.000 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

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10879059641262569160704.000000 (between atoms 4029 and 4030) rms 157073328433382031360.000000
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
    933    935   38.7    0.1330   0.1811      0.1330
    935    936   41.3    0.1000   0.1411      0.1000

................so much atoms number

   4210   4212   52.3    0.1330   0.2032      0.1330
   4212   4213   30.8    0.1000   0.1209      0.1000

Wrote pdb files with previous and current coordinates
[localhost:09678] *** Process received signal ***
[localhost:09678] Signal: Segmentation fault (11)
[localhost:09678] Signal code: Address not mapped (1)
[localhost:09678] Failing at address: 0x5ad01b00
[localhost:09678] [ 0] /lib/tls/libpthread.so.0 [0xab68b0]
[localhost:09678] [ 1] mdrun(do_nonbonded+0x349) [0x816d4a1]
[localhost:09678] *** End of error message ***
Segmentation fault


 I have been trying to solve this problem for quite some time now. It  would be very helpful if you can suggest some way to work around  this problem.
thanks!

jianlu guo
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