[gmx-users] Re:The X-size of the box times triclinic skew factor

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 26 13:41:30 CEST 2009

wuxiao wrote:
> Dear Mark,
>    Thank you for your reply. The system I simulated was one Polymer 
> chain solvated by 200 water  that had totally about 3000 atoms. I had 
> defined the system density as 1000 using editconf.

That just does a scaling. It might not fix a gross problem, so do look
at the box dimensions before and after.

> This density was very 
> the experimental one. After enough minimization (convergent to 0.1 
> kj/mol) and 3 ns of NVT MD, the NPT MD was performed as describe in the 
> original question. It happened to terminate with the fatal error after 
> about 300 ps. It should be noted that I ran the mpimdrun using the 
> following command:
> mpirun -np 4 mpimdrun -s 03md.tpr -c poly_md.gro -v
> I have a four-core CPU. Can you give more help according to these 
> descriptions?

Your preparation seems good enough not to be the source of the problem.

Have a look at the trajectory. What does the structure look like? What
is happening to the box dimensions and/or density (look in the .log file
and/or use g_energy)?.

I believe that the error message you're getting is consistent with a
drastic decrease in the box size. Since EM and NVT don't break and NPT
does, the most likely hypothesis is that it started far too large.


> Best regards,
> xiaowu
> wuxiao wrote:
>  > >Dear gmx users,
>  > >While doing a NPT molecular dynamics(MD), A fatal error was given:
>  > >The X-size of the box times triclinic skew factor is smaller than the
>  > >number of DD cells times the smallest allowed cell size.
>  > >However, either NVT or NVE MD can work well. Can you give any help to
>  > >deal with this problem?
>  >It sounds like you might have started with a density that is too low for
>  >your box size.
>  >A more complete description of your system and what you've done with it
>  >might help you get useful advice.
> Mark
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