[gmx-users] mdrun WARING and crash

[Justin Lemkul]

On 3/12/13 5:14 AM, L.Liu at utwente.nl wrote:
> Hallo Justin,
>
> Thank you for your reply, I uploaded the images, Please find following the link below,
>
> start box:
> http://s1279.beta.photobucket.com/user/Li_Liu/media/image0_zpsf95d10fe.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publicOnly]=1&sort=1&o=1
>
> and  snapshot for first step:
> http://s1279.beta.photobucket.com/user/Li_Liu/media/image1_zps06f589e6.jpeg.html?filters[user]=134822327&filters[recent]=1&filters[publicOnly]=1&sort=1&o=0
>

Whatever physical model you are using is causing the particles to become 
regularly arranged.  There's no problem from the Gromacs side that I can see. 
The problem is in your setup (i.e. force field) or its use.  On that matter, I 
cannot comment.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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