> hello: > > I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day.... here is the script I used for > submitting jobs: > > # @ job_name = gmx_test > # @ class = kdm-large > # @ error = gmx_test.err > # @ output = gmx_test.out > # @ wall_clock_limit = 00:20:00 > # @ job_type = bluegene > # @ bg_size = 32 > # @ queue > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes > -v -s npt > _01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt" -mode > VN -np 128 > > > > here is my npt.mdp > > title = NPT-01 > cpp = /usr/bin/cpp > include = > define = -DPOSRES -DPOSRES_POPE_HEAD > integrator = md > dt = 0.001 > nsteps = 5000000 > nstxout = 100000 > nstvout = 100000 > nstlog = 100000 > nstenergy = 50000 > nstxtcout = 50000 > xtc_grps = > energygrps = Protein SOL ION > nstcalcenergy = 10 > nstlist = 10 > nstcomm = 10 > comm_mode = Linear > comm-grps = Protein_POPE Water_and_ions > ns_type = grid > rlist = 1.2 > rlistlong = 1.4 > vdwtype = Switch > rvdw = 1.2 > rvdw_switch = 0.8 > coulombtype = pme > rcoulomb = 1.2 > rcoulomb_switch = 0.0 > fourierspacing = 0.15 > pme_order = 6 > DispCorr = no > tcoupl = V-rescale ;nose-hoover > nhchainlength = 1 > tc-grps = Protein_POPE Water_and_ions > tau_t = 0.1 0.1 > ref_t = 310 310 > Pcoupl = berendsen ;parrinello-rahman > Pcoupltype = semiisotropic > tau_p = 1.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > pbc = xyz > refcoord_scaling = com > gen_vel = no > optimize_fft = no > constraints = hbonds > constraint_algorithm = Lincs > > Does anybody have any advices?
Albert - What is the speed using serial gromacs for the same system? Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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