[gmx-users] problem with LINCS

[Justin A. Lemkul]

Thomas Koller wrote:
> Hello!
> 
> I have the following problem:
> 
> I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps after the volume equilibration, I got this message:
> 
> Step 2160, time 4.32 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 2702.127453, max 65115.246094 (between atoms 130 and 131)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     121    123   91.9    0.1378   0.6015      0.1378
>     130    131   90.0    0.1526 9936.7393     0.1526
>     ...
> 
> I use LINCS with h-angles. 
> 
> The whole procedure works when I don't use the conformer pair, but two separate ions inserting randomly in the box. I get no LINCS warning. What can be the problem?
> 

Hard to say.  What does the trajectory show?  How successful was energy 
minimization, and what were your criteria?  What's in your .mdp file?

Additional troubleshooting points can be found here:

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

-Justin

> Regards and thanks,
> Thomas
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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