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

wuxiao xiaowu759 at hotmail.com
Sun Apr 26 13:23:24 CEST 2009

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. 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?

Best regards,



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.

MSN 表情魔法书,改变你的对话时代!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090426/1982e84b/attachment.html>

More information about the gromacs.org_gmx-users mailing list