Hi Albert, You are doing neighboursearching every step! So every step all 200 CPUs need to know the how and what of all the other 199. Imagine the communication overhead. Furthermore, you have 400 atoms per CPU (neglecting the PME dedication). That will also make communication a bottle neck. Which, incidentally, will show up when you finish or terminate the run. According to the md.mdp you posted you're also using a 1fs time step rather than 2fs. Try decreasing the number of CPUs, and increasing nst*. Maybe you can get much better performance if you have an 8- or 12-core around and use a single machine. Certainly pays off if you need to do replicate runs anyway.
Cheers, Tsjerk On Wed, Mar 28, 2012 at 5:31 PM, Albert <[email protected]> wrote: > Dear: > > 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 > > > > Thank you very much > > best > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands
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