[gmx-users] System broken after energy minimization

[Justin Lemkul]

On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote:
> Dear users,
>
> I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
> after minimizing, the system have been crashed. I do not understand why. I
> attach the em.mdp below
>

The list does not allow attachments.  Either copy and paste or provide a link to 
where the file can be downloaded.  The .mdp file may or may not be useful.  You 
should carefully inspect the starting configuration for atomic overlap, and then 
otherwise follow the instructions described here:

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

-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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