Hi, On Mon, May 16, 2016 at 9:13 PM <khourshaeisha...@mech.sharif.ir> wrote:
> > > <style type="text/css"> > p { margin-bottom: 0.1in; line-height: 120%; }a:link { }</style> > > > Dear Gromacs users > > > During simulating DPPC membrane I confront with several Problems. I > intend to express them here and I really appreciate it if you help me. > Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC > molecules. the trend ( I mean the way it increase or decrease) of > Pressure xx is important to me. as one can expect, due to the size of my > system ( number of atom) the result is so erratic ( about 200bar). > so I enlarge the system in X-direction considering consistent trend for > both system. so I replicated system in X-direction, minimized it and do > an NPT on it. > A common mistake here is to concatenate boxes without leaving a suitable spacing between them, because atoms whose centers are close to the old edges of the box can now be too close to their new neighbours. > during NPT, my working job blew up with this error : > > > An atom moved too far between two domain decomposition steps > > > does this error relate to the number of cpu-cores, because when I > decrease number of the cores from 16 to 8 using -nb 8, I don't see > this error again, but there is no progress in the number of steps !!! > Different parallelism leads to different forces, and (in this case) different ways for the simulation to blow up, particularly if my guess is correct. > also I have question about MPI. In my laptop when I simulate a box > ( 128 > DPPC with 2000 W), the system runs with : > > > Using 1 MPI thread > > Using 4 OpenMP threads > > > when I do the same, in High performance Computer of the > university, Its > output is totally different which also uses automatically : > > > Using 24 MPI threads > > Using 1 OpenMP thread per tMPI thread > > > but when I used -ntmpi 1 to change MPI threads to 1, it gave the > same > answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I > should notice that I now what is the meaning of MPI and thread, but > don't now what is the optimum number !!!! > It varies. mdrun has some heuristics that consider the kind of processor, the number of cores, the number of atoms, the presence of GPUs, the value of environment variables like OMP_NUM_THREADS... Mark > > best regards > > > Ali > > > ================== > > > Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) > > > Department of Mechanical Engineering > > > Sharif University of Technology, Tehran, Iran > > > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.