[gmx-users] Signal: Segmentation faul

[Justin A. Lemkul]

shikha agarwal wrote:
> hi,
> HAPPY NEW YEAR
> 
> I am experiencing a segmentation fault during mdrun in equlibration step .
> error
> 
> Wrote pdb files with previous and current coordinates
> [shikha-desktop:01719] *** Process received signal ***
> [shikha-desktop:01719] Signal: Segmentation fault (11)
> [shikha-desktop:01719] Signal code: Address not mapped (1)
> [shikha-desktop:01719] Failing at address: 0x8d22a70
> [shikha-desktop:01719] [ 0] [0xb87410]
> [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]
> [shikha-desktop:01719] *** End of error message ***
> Segmentation fault
> 
> 
> 
> 
> 
> bottom lines of my .log file after energy minimization is this
> 
> 
> 
>  Step           Time         Lambda
>           11357    11357.00000        0.00000
> 
>            Step           Time         Lambda
>           11358    11358.00000        0.00000
> 
>            Step           Time         Lambda
>           11359    11359.00000        0.00000
> 
>            Step           Time         Lambda
>           11360    11360.00000        0.00000
> 
>            Step           Time         Lambda
>           11361    11361.00000        0.00000
> 
> 
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> Steepest Descents converged to machine precision in 11362 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -5.4871900e+06
> Maximum force     =  3.9830833e+03 on atom 4511
> Norm of force     =  1.9521437e+01
> 

Well, EM completed, but the forces are still very high, indicating that the 
system is likely not yet stable.  Look at the structure to see what might be 
causing problems around atom 4511.

-Justin

-- 
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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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