[gmx-users] how to understand this sentence

[lina]

On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 1/12/2011 3:25 AM, lina wrote:
>>
>> The Y-size of the box (1.999239) times the triclinic skew factor
>> (1.000000) is smaller than the number of DD cells (2) times the
>> smallest allowed cell size (1.000000)
>>
>> I don't understand the fatal error message it has been given during a
>> simple run,
>>
>> I tested with large box already, during editconf I used -d 30 already,
>>
>> it's a very small peptide, the box dimension is   63.95000  60.76600
>>  62.9990
>
> Your system may be too small to parallelize over the number of processors
> you are using (and as usual, it would have been a good idea to supply your
> mdrun command line unless you enjoy wasting time when people make wrong
> guesses).

As you can see it's a very small job, so I just run on laptop,

now I changed the mdrun -nt 4
it showed:
Fatal error:
The X-size of the box (3.994507) times the triclinic skew factor
(1.000000) is smaller than the number of DD cells (4) times the
smallest allowed cell size (1.000000)


The Fatal error about the Y-size when I used mdrun -nt 8

can you guess which is wrong here. on the last email the URL contains
the md.mdp, topol.top and .gro files to run a mdrun.

Thanks,

>
> Mark
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