[gmx-users] Fatal error:;Too many LINCS warnings (10716)

[Mark Abraham]

E.Elavazhagan wrote:
> Hai folks,
> Thanks for ur previous valuable suggestions.
> 
> On executing the mdrun command we get the following error.
>  mdrun -v -s pr -e pr -o pr -c after_pr -nice +5 -g pr_log
> 
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: clincs.c, line: 559
> 
> Fatal error:
> Too many LINCS warnings (10716) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently 
> equilibrated,or if yo
> u 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.
> 
> Then we tried by changing the Berendsen temp coupling with Nose-Hoover 
> temp coupling also the pme_order 6 to lower values.

This will be irrelevant in all likely scenarios.

> On the manual 3.2 the lamda value is in the range of 0.8to 1.25.Let us 
> come to know where can we do these lamda alternation or how to tackle 
> this problem .Herewith I have attached my pr.mdp file for ur kind glance.

There are two possibilities listed in the helpful error message. What 
makes you think your system is sufficiently equilibrated?

Mark