Dear Karim, a (small) load imbalance is perfectly normal for a parallel simulation and no need to switch over to particle decomposition (both domain and particle decomposition should however work). Are you shure you get no error message? People will need some more information here to be able to help. It is usually a good idea to include which MPI lib you are using and the exact command line how you invoked mdrun. You could anyway try to run on a single processor only and see whether this scenario also "stops" or whether you get a proper error message or core file.
Carsten On Dec 22, 2010, at 12:34 PM, Mahnam wrote: > In God We Trust > Hello Dear GMX users > I want to do MD on one peptide in water with gromacs 4.5.3. > I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I > do final mdrun it has load imbalance and when I try -pd option it stops > after 265 ps without any error massage !, can everybody help me. > Here is my mdp file . > constraints = hbonds > integrator = md > dt = 0.002 > nsteps = 50000000 > nstcomm = 10 > comm_mode = Linear > comm_grps = protein > nstxout = 250 > nstvout = 1000 > nstfout = 0 > nstcalcenergy = 10 > nstlog = 1000 > nstenergy = 1000 > nstlist = 10 > ns_type = grid > rlist = 1.2 > coulombtype = PME > rcoulomb = 1.2 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > energygrps = protein SOL > > > ; Berendsen temperature coupling is on in three groups > Tcoupl = v-rescale > tau_t = 0.1 1 > tc-grps = protein bulk > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = parrinello-Rahman > tau_p = 1 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > > Many thanks in advance for your help and your reply. > Yours truly > Karim Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran University > P.O.box 13145-1384 > Tehran > Iran > http://www.ibb.ut.ac.ir/ > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists