[gmx-users] Re: Charge group moving too much

[Vitaly V. Chaban]

Hi,

The easiest way to fix the problem is to decrease the current
timestep. Also please read about -dd and -rdd keys of mdrun utility.

Vitaly


> One of my simulations just crashed after 660,000 steps with the
> following message:
>
> Step 660560:
> The charge group starting at atom 4100 moved than the distance allowed
> by the domain decomposition (1.500000) in direction X
> distance out of cell 2.356293
> Old coordinates:    1.752    0.447    0.751
> New coordinates:    3.593    1.532    0.674
> Old cell boundaries in direction X:    0.000    2.116
> New cell boundaries in direction X:    0.000    2.122
>
> -------------------------------------------------------
> Program mdrun, 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
> -------------------------------------------------------
>
> "Why Weren't You at My Funeral ?" (G. Groenhof)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun on CPU 0 out of 8
>
> I am modelling flexible alkyl chains which are anchored to a frozen
> silica wall. This particular atom (4100) is at the edge of the
> periodic boundary condition so I am guessing that what happens is that
> while the anchored side stays where it is, the other free end wanders
> into the next cell and this perhaps triggers the error message? If
> this is indeed the problem, is there some way to stop the program
> stopping with an error message when this happens?
>
> I did do an energy minimisation before starting and my structure looks
> OK. It seems strange that it would crash only after 660000 steps.
>
> Also what is meant by the following? I am using NVT so my simulation
> cell should not change.
>
> Old cell boundaries in direction X:    0.000    2.116
> New cell boundaries in direction X:    0.000    2.122
>
>
> My cell is about 4.3 x 4.3 x 7.5 nm
> I am using gromacs-4.0.5
>
> Thanks