[gmx-users] Bad water sampling ? => A charge group moved too far between two domain decomposition steps ???

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> The system is "one lysozyme + water " running on 16 nodes.
> 
> 
> After => Energy minimization of the solvated systemRelaxation of solvent and
> hydrogen atom positions: Position restrained MDThen, the error was shown.
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec.c, line: 3651
> 
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> -------------------------------------------------------
> 
> 
> The energy minimization is as follows
> 
> ; Parameters describing what to do, when to stop and what to save
> integrator	= steep		; Algorithm (steep = steepest descent minimization)
> emtol		= 1.0		; Stop minimization when the maximum force < 1.0 kJ/mol
> nsteps		= 500000		; Maximum number of (minimization) steps to perform
> nstenergy	= 1		; Write energies to disk every nstenergy steps
> energygrps	= System	; Which energy group(s) to write to disk
> 
> 
> 
> But, the above error is still there.
> My understanding is that "A charge group moved too far between two domain
> decomposition steps" comes from the bad water sampling. The bad water
> sampling will make the charge groups too close. The, they are against each
> other sharply and leave each other with a high speed.

That's possible, but there are other similar hypotheses.

I posted some coping strategies earlier today that are also applicable 
here. If you have a well-formed system, then perhaps you just need to be 
gentler with it.

Mark