[gmx-users] segmentation fault with lincs warning

[Justin A. Lemkul]

ANINDITA GAYEN wrote:
> Dear all,
> 
> 
> I have an dmpc bilayer equilibrated for 12 ns. I have built a CHAPS molecule in the OPLSAA force field and inserted it in the equilibrated bilayer. There was no problem till the minimisation, but when i started the MD, the job escaped out with a lincs error
> 
> Initializing LINear Constraint Solver
>   number of constraints is 6572
>   average number of constraints coupled to one constraint is 3.3
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.817519   4126   4128   0.017115
>         After LINCS         30.145958  17066  17068   1.789056
> 
> 
> Step -2, time -0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 30.145958 (between atoms 17066 and 17068) rms 1.789056
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4128   4129   31.1    0.1571   0.1600      0.1530
>   16859  16858   36.1    0.1529   0.1022      0.1529
>   16858  16859   36.1    0.1529   0.1022      0.1529
>   16897  16858   49.2    0.1523   0.1495      0.1529
> [all the atoms and bonds in the error list are for CHAPS]
> 
> Do i have the problem in the topology file? I have inserted 4 chaps mole cules without replacing the dmpc molecules, i.e. 4 chaps with 128 dmpc molecules in the bilayer. Is this causing any steric problem?
> 

This is a *very* common problem, and a lot of potential solutions are in the 
list archive and wiki site.  As such, I won't list them here, but you can 
certainly find them within a few minutes (or seconds) of searching.

If you have a pre-equilibrated bilayer, and inserted molecules into it without 
removing any lipids, you probably have very severe atomic overlap.  But as I 
said, search the archive and try the things you find there.

-Justin

> Please suggest a way to get out of the problem. If you want, i can upload my topology and mdp files in the next mail.
> 
> Yours truly,
> anindita gayen
> 
> 
> 
> 
> 
> 
>       Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
> 
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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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