[gmx-users] lambda

[Mark Abraham]

? wrote:
> Hi everybody,
>  
> I  try to  calculate a protein which has two chains.This chains  has 
> sulphide bridges between eachother.I used -merge in pdb2gmx.I calculated 
> for 20ns.I said free energy:no.
>  
> But I got this error:
>  
> /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.
> />/
> I looked at mailing list.Idecided to change /delta-lambda=0.00002
> Can anyone help me about this?

Please search the mailing list for help in future. This problem is the 
most frequently reported one, and the most frequent cause is exactly 
what it says "your system is not sufficiently equilibrated"

Mark