[gmx-developers] Error with octahedral box and domain decomposition in CVS-version

[Jochen Hub]

Hi Berk,

thanks for the quick reply. You were right, the error does NOT occur in 
a recent Version (3.3.99_development_20080208). I was using an oder 
CVS-Version (3.3.99_development_20070618) from last summer.

thanks again,
Jochen

Berk Hess wrote:
> Hi,
>
> Since you mention the current CVS version, I assume you are using an 
> old version.
> From when is that version?
> There have been loads of bugs in CVS, but we are using the current 
> version
> without problems.
>
> Berk.
>
> Jochen Hub wrote:
>> Hi,
>>
>> when running a octahedral system of 31779 atoms on 16 or 8 CPUs with 
>> domain decomposition I am getting the errors like shown below. Is 
>> that a known problem or has it even been fixed in the current  CVS 
>> version? Should I submit a bugzilla? Playing with the -dd parameters 
>> or switching -dbl on an off did not help. Btw, the charge group which 
>> seems to move too rapidly is always a water molecule. The system 
>> (protein+water+ions) is OK, it is runnig without problems in gromacs 
>> 3.3.1.
>>
>> Cheers, Jochen
>>
>>
>> Making 3D domain decomposition 2 x 2 x 2
>> starting mdrun 'Protein'
>> 100000000 steps, 200000.0 ps.
>>
>> step 0
>>
>> Step 30:
>> The charge group starting at atom 21975 moved more than the cut-off 
>> (1.000000) in direction x
>> distance out of cell -1.110520
>> Old coordinates:    0.602    1.641    0.007
>> New coordinates:   -1.668    4.849    5.566
>> Old cell boundaries in direction x:    0.000    3.257
>> New cell boundaries in direction x:    0.000    3.225
>> -------------------------------------------------------
>> Program mdrun, VERSION 3.3.99_development_20070618
>> Source code file: domdec.c, line: 1806
>>
>> Fatal error:
>> A charge group move too far between two domain decomposition steps
>> -------------------------------------------------------
>>
>>
>>
>
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************