[gmx-users] how to understand this sentence

[lina]

Now I used mdrun -nt 2

it showed:

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.

and mdrun -nt 1 it showed:

Program mdrun, VERSION 4.5.4-dev-20110711-dadcb
Source code file:
/var/local/cache/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.


On Thu, Dec 1, 2011 at 11:38 AM, lina <lina.lastname at gmail.com> wrote:
> 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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>