[gmx-users] LINCS WARNING

[Dallas B. Warren]

>     I am runing a MD of protein. Now I see some warning 
> message on screen,I don't know how to understand it , Could 
> somebody tell me about it? Thank you very much!

It means that the bond between the two atoms listed there is moving too
far in each time step.  The reason for that problem can greatly vary.
What it does mean is that something is wrong, either with the parameters
or interactions in that region of the simulation, the settings used for
running the simulation, or the structure in that region.

Perform a search of the emailing list using that error message, and you
will come up with a significant number of emails explaining it further,
solutions etc.

Such as these:
	http://www.gromacs.org/pipermail/gmx-users/2003-May/005335.html
	
http://www.gromacs.org/pipermail/gmx-users/2006-March/020477.html
	http://www.gromacs.org/pipermail/gmx-users/2006-July/022578.html

Plus many, many more.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.