[gmx-users] system exploid during running

[Justin A. Lemkul]

Morteza Khabiri wrote:
> Dear gmxuser
> 
> Thanks for your advices. Because of your help I could run my solution and
> protein together.
> but during the run I faced with this warning which cause the run again be
> crashed, The message is:
> 
> relative constraint deviation after LINCS:
> max 0.000615 (between atoms 1731 and 1732) rms 0.000023
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1731   1732   30.7    0.1000   0.0999      0.1000
> 
> do anybody knows what should I do now?
> 

Is this happening during minimization, equilibration, or the production phase?

Did minimization succeed?  If so, what was the potential energy and maximum 
force?  What kind of equilibration are you attempting?

What are you specifying in your .mdp file?

What does the trajectory show?  Did it write any frames that might point to the 
beginning of the problem?

You can also search the list archive for "LINCS warning," and you will see 
several hundred posts showing the same problem, and potential solutions.  Also 
look at these relevant wiki entries:

http://wiki.gromacs.org/index.php/blowing_up

http://wiki.gromacs.org/index.php/error#LINCS.2FSETTLE.2FSHAKE_warnings

-Justin

> Thanks
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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