[gmx-users] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

Lan Hua wrote:
> Hi Justin,
> 
>    I took all your suggestions. But the same thing happened again in the 
> NPT step with the "Segmentation fault" for some starting structure.  I 
> attached the mdp file I used.  Do you have any idea what else could 
> cause this error?
> 
>    Thank you very much!
> 

The only advice I can give is here (with special attention to the "Diagnosing an 
Unstable System" section):

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I know you have explained your reasoning for using version 3.1.4, but do realize 
that there have been numerous bug fixes and feature upgrades in the last 8 
(yikes!) years of Gromacs development that may affect stability.  I have never 
used 3.1.4, so if there's some inherent issue with that version, you can also 
check the list archive for anyone that had similar issues back when 3.1.4 was 
actually a recent release.

-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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