[gmx-users] error:Segmentation fault

[Mark Abraham]

¹ù½¨Â· wrote:
> 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!

The standard advice is here http://oldwiki.gromacs.org/index.php/blowing_up

Mark