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Dear Mark,<BR>
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:<BR>
mpirun -np 4 mpimdrun -s 03md.tpr -c poly_md.gro -v<BR>
I have a four-core CPU. Can you give more help according to these descriptions?<BR>
Best regards,<BR>
xiaowu<BR>
<BR>
wuxiao wrote:<BR>> >Dear gmx users,<BR>> >While doing a NPT molecular dynamics(MD), A fatal error was given:<BR>> >The X-size of the box times triclinic skew factor is smaller than the <BR>> >number of DD cells times the smallest allowed cell size.<BR>> >However, either NVT or NVE MD can work well. Can you give any help to <BR>> >deal with this problem?<BR> <BR>>It sounds like you might have started with a density that is too low for<BR>>your box size.<BR> <BR>>A more complete description of your system and what you've done with it<BR>>might help you get useful advice.<BR> <BR>Mark<BR><BR><br /><hr />立刻下载 MSN 保护盾，保障Messenger 安全稳定！ <a href='http://im.live.cn/safe/' target='_new'>现在就下载！</a></body>
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