[gmx-users] LINCS

teklebrh at ualberta.ca teklebrh at ualberta.ca
Thu Aug 27 22:05:32 CEST 2009

Hi Justin,

"There is something physically unrealistic about your model"

You are right!

The main problem I found out is that some of the structures in my  
Solution broke down......

I used ...

genbox -cp XXXX.grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top  

To generate multiple structures in a box. However, it creates overlap  
and my orginal structures broke down. I checked the structures!

Can you please let me how to generate multiple structures in a fixed  
box at random or packed in a solutio (e.g water)

Thank you for you help


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> teklebrh at ualberta.ca wrote:
>> Hi Justin,
>> I tried to run full MD after energy minimization in both vacuo and  
>> water... went good but I got this ERROR once I try to run full MD.
>> Can you please help.....
> There is something physically unrealistic about your model.  That's  
> the case whenever you see a LINCS warning.  Without a more complete  
> description of what you've done (minimization and equilibration  
> protocol, initial construction of the model, etc) and the details of  
> your simulation parameters, there's nothing more anyone can really  
> say beyond a guess.
> It appears that the wiki is down at the moment, but these pages have  
> useful information (when the site comes back up):
> http://oldwiki.gromacs.org/index.php/blowing_up
> http://oldwiki.gromacs.org/index.php/Errors
> And since LINCS errors have been posted thousands of times to the  
> list, the archive should have some useful advice as well, so search  
> here:
> http://oldwww.gromacs.org/swish-e/search/search2.php
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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