[gmx-users] system exploid during running

[Manoj Singh]

I think system is not properly minimized. Try minimizing it first using
l-bfgs (very helpful in these cases)  followed by steep or conj. Make sure
you are getting unrestrained minimization before running MD simulation.

On Mon, Sep 15, 2008 at 11:13 AM, Morteza Khabiri <khabiri at greentech.cz>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?
>
> Thanks
>
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