[gmx-users] segmentation fault

[Justin A. Lemkul]

Quoting Magnus Andersson <magnus.andersson at chalmers.se>:

> Hi all,
>
> My constrained 20ps simulation crashes for some reason. This simulation is
> very much alike other simulations I've run in a successful manner
> previously. Seems like there is a probem on atoms constituting an
> artificial membrane...
>
> Anyway, I guess it is a general question. Where do you start looking if
> the run crashes like this (and a slightly different system, just strctural
> change, it has exactly the same atoms...)?
>
> Error message looks like=
>
> step 340, will finish at Tue Dec 11 12:52:51 2007
> Step 344, time 0.688 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000822 (between atoms 2262 and 2263) rms 0.000041
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    2262   2263   42.4    0.1090   0.1089      0.1090
>    2265   2266   30.3    0.1090   0.1090      0.1090
>
> Step 345, time 0.69 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.001312 (between atoms 2265 and 2266) rms 0.000051
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    2262   2263   30.0    0.1089   0

In my experience, looking at the atoms LINCS is complaining about is a good
place to start.  I've seen these warnings when I have somehow generated a
structure with bad contacts.  Thorough energy-minimization and gentle
equilibration usually alleviates the problem.

-Justin

>
> Thankful for a reply /
>
> Magnus Andersson
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
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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