[gmx-users] bonds that rotated more than 30 degrees:

[Justin A. Lemkul]

Yanmei Song wrote:
> Dear Users:
> 
> I used all-bonds for constraints. My MD is dead right after i submit the 
> task. The error message is :
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.084475 (between atoms 23417 and 23431) rms 0.054595
> bonds that rotated more than 30 degrees:
> 
> Anyone knows what is the problem and how i can fix it?

Please see the following:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Beyond that, search the list archive - this error comes up almost daily, and 
there are plenty of solutions to try.  If you still can't find a solution, post 
a detail description of your system, including how you built it, what you've 
done to energy-minimize and/or equilibrate it, and post the contents of any 
relevant .mdp file(s).

-Justin

> Thanks
>  
> 
> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
> 
> 
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-- 
========================================

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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