> I am using gromacs for membrane simulation (under CHARMM36 FF) which > contains around 80,000 atoms. I've submitted over 200 CPU in the cluster > for such system with 2 fs time step. And what really astonished is that the > efficiency for such simulation is only 3ns/day..... I am wondering what > happen to my system or gromacs? What can I do to fasten the simulation? > > here is my md.mdp: > * > title = god! > cpp = /usr/bin/cpp > include = > define = > integrator = md > dt = 0.001 > nsteps = 100000000 > nstxout = 1000000 > nstvout = 1000000 > nstlog = 1000000 > nstenergy = 10000 > nstxtcout = 100000 > xtc_grps = > energygrps = Protein POPC SOL ION > nstcalcenergy = 1 > nstlist = 1 > nstcomm = 1 > comm_mode = Linear > comm-grps = Protein_POPC 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 = 4 > DispCorr = no > tcoupl = nose-hoover > nhchainlength = 1 > tc-grps = Protein_POPC Water_and_ions > tau_t = 0.5 0.5 > ref_t = 310 310 > Pcoupl = parrinello-rahman > Pcoupltype = semiisotropic > tau_p = 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > pbc = xyz > gen_vel = no > optimize_fft = no > constraints = hbonds > constraint_algorithm = Lincs > *
This discussion should be started with you reporting the speedup for your system with 200cpu's. Rather than appealing just to some velocity per nanosecond. Neighborsearching is inefficient. Outputting immediate velocities every 1000000 steps is senseless. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 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
