[gmx-users] system exploid during running
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 15 17:57:34 CEST 2008
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:
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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