[gmx-users] clashes

[Justin A. Lemkul]

Dariush Mohammadyani wrote:
> Yes, you are right. I made a mistake to write an error:
>  
> [n0017:07436] *** Process received signal ***
> [n0017:07436] Signal: Segmentation fault (11)
> [n0017:07436] Signal code: Address not mapped (1)
> [n0017:07436] Failing at address: 0x1d620d20
> 
>  
> 
> What do you mean for "Better energy minimization"?
> 

Your system is likely blowing up.

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

Something has become physically unstable, which is usually due to incorrect .mdp 
parameters for the run that lead to the breakdown of the physical model or (more 
commonly) the simulation was not initialized from a suitably low-energy state, 
implying either insufficient minimization (i.e. Fmax was too high) or inadequate 
equilibration.

-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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