[gmx-users] LINCS warning in md run

[Justin Lemkul]

On 9/12/12 6:57 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> during the mdrun_mpi I get many LINCS warnings like for example:
>
> Step 1143, time 1.143 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.265373, max 1.416702 (between atoms 976 and 979)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      976    979   90.0    0.1072   0.2320      0.0960
>
>
> But I don't know why. I already minimized my protein. And also in the
> grompp run there were no error messages. This was the end of my grompp
> output:
>
>
> processing index file...
> Making dummy/rest group for Acceleration containing 80212 elements
> Making dummy/rest group for Freeze containing 51274 elements
> Making dummy/rest group for VCM containing 80212 elements
> Number of degrees of freedom in T-Coupling group System is 102623.00
> Making dummy/rest group for User1 containing 80212 elements
> Making dummy/rest group for User2 containing 80212 elements
> Making dummy/rest group for XTC containing 80212 elements
> Making dummy/rest group for Or. Res. Fit containing 80212 elements
> Making dummy/rest group for QMMM containing 80212 elements
> T-Coupling       has 1 element(s): System
> Energy Mon.      has 2 element(s): Protein non-Protein
> Acceleration     has 1 element(s): rest
> Freeze           has 2 element(s): Protein_&_!TYP rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): rest
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> Estimate for the relative computational load of the PME mesh part: 0.32
> writing run input file...
>
>
> Can you please help me?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Without a complete description of your system (its contents, previous 
minimization and equilibration and their success/failure) and any relevant .mdp 
file(s), there's little else that anyone can say.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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