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
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