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. Mark > 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 > > > ------------------------------------------------------------------------ > 立刻下载 MSN 保护盾，保障Messenger 安全稳定！ 现在就下载！ > <http://im.live.cn/safe/> > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
