[gmx-users] Charge group moving too much

[Jennifer Williams]

Hello,

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




-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.