Thanks Justin. I think you are right. I always encounter this problem with extremely small runs.
On Tue, Jun 8, 2010 at 11:04 AM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > >> Hi, >> >> I am running a very short md run for 100 steps and I get the Infinite giga >> flopses error. I stored info at every step to check if the simulation is >> running. And the log file has all the variables for each time-step with >> reasonable values. I don't understand the meaning of the message at the end >> of the log file. >> nodetime = 0! Infinite Giga flopses! >> Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 >> >> This is not the first time I have encountered this problem with short md >> runs. >> >> > This isn't really a "problem," per se. Gromacs is fast. If you look at > the benchmarks in the Gromacs 4 paper, you can get several hundred steps of > MD per second for a relatively small system. So essentially your run > probably finished in less than a second, and mdrun recorded that as "zero" > time. Division by zero = infinite performance :) > > If you think there's something else actually wrong, please at least provide > a description of how large your system is, how long the run actually took to > complete, if you're running in parallel, etc. > > -Justin > > > Parameter file >> >> ; VARIOUS PREPROCESSING OPTIONS title =NPT simulation >> for a 2D WCA system >> cpp =/lib/cpp >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.0001 >> nsteps = 100 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 0 ; No output, except for last frame >> (coordinates) >> nstvout = 0 ; No output, except for last frame >> (velocities) >> nstfout = 0 ; No output, except for last frame >> (forces) >> nstlog = 1 ; Write every nth step to the log >> nstenergy = 0 ; Write energies at every n step >> nstxtcout = 0 ; Do not write a compressed tr >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = Cut-off >> rcoulomb = 1.1225 >> vdw-type = Cut-off >> rvdw = 1.1225 >> >> ; Temperature coupling >> tcoupl = v-rescale >> tc-grps = AR >> tau_t = 0.1 >> ref_t = 0.1 >> ld_seed =-1 >> >> ; Pressure coupling >> pcoupl = Berendsen >> pcoupltype = semiisotropic >> tau-p = 0.1 0.1 >> compressibility = 1e-5 0 ;Dont know >> ref-p = 58 0 >> >> >> ;Generate velocities for startup run >> gen_vel =yes >> gen_temp =1 >> gen_seed =-1 >> >> ;Non equilibrium MD steps >> freezegrps =AR >> freezedim =N N Y >> >> Error: At the end of log file >> >> nodetime = 0! Infinite Giga flopses! >> Finished mdrun on node 0 Tue Jun 8 10:16:31 2010 >> >> >> Regards >> Pooja >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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