[gmx-users] Too many LINCS warning

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 26 13:24:39 CEST 2008

vivek sharma wrote:
> Hi There,
> I am trying to scale my system(system with 45000 atoms which is one 
> protein molecule in water box) to run on more number of processor
> I have asked a number of related queries, but now I am getting warning 
> pasted below...
> Fatal error:
> Too many LINCS warnings (11587) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently 
> equilibrated,or if you are changing lambda too fast in free energy 
> simulations.
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file, but normally it is better to fix the problem.
> and the same run is running well with 20 processor, but I got the error 
> pasted above in aan attempt to run the same problem for 40 
> processor...and it followed by writing the intermediate step.pdb
> Can anybody suggest how should I tackle the problem, and what other 
> option I can try in this scenario ?

I have seen this too, when I try to use too many processors.  I don't know the 
reason.  Did you adhere to my previous advice (regarding Gromacs 3.3.x, you 
still haven't told us which version of Gromacs you're using):

Max # of CPU = (total atoms)/(protein atoms)?

The goal is to keep the load evenly distributed over nodes.  The above is not 
necessarily necessary under 4.0rc1 with the advent of P-LINCS.


> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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