[gmx-users] System broken after energy minimization

[Tsjerk Wassenaar]

Hey :

When increasing the system size like that, make sure that all molecules in
the original box are whole (trjconv -pbc mol). Only then can you, e.g., use
genconf to double the system.

Cheers,

Tsjerk


On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System>
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.