Mark, Your are right. Thanks
Daniel 2009/9/24 Mark Abraham <mark.abra...@anu.edu.au>: > Daniel Adriano Silva M wrote: >> >> Dear GROMACS users and developers. >> >> I don known if this issued had been previously addressed, but I found >> that when I try to run a MD with time-step of 2fs and 2500000000 steps >> (yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX >> and icc 10 compiler): >> >> #################### >> WARNING: This run will generate roughly 20576946697451257856 Mb of data >> >> starting mdrun 'F1-ATPASE' >> -1794967296 steps, -3589934.8 ps. >> >> nodetime = 0! Infinite Giga flopses! >> Parallel run - timing based on wallclock. >> >> ##################### >> >> If i reduce the steps number by one order of magnitude then all goes >> ok. My MDP when I obtined this error was: >> >> >> ; VARIOUS PREPROCESSING OPTIONS >> title = NPT simulacion >> cpp = /lib/cpp >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.002 >> nsteps = 2500000000 >> nstxout = 5000 >> nstvout = 5000 >> nstlog = 2500 >> nstenergy = 2500 >> nstxtcout = 2500 >> energygrps = Protein Non-Protein >> nstlist = 10 >> rlist = 1.0 >> ns_type = grid >> pbc = xyz >> coulombtype = pme >> rcoulomb = 1.0 >> vdw-type = Cut-off >> rvdw = 1.0 >> fourierspacing = 0.12 >> pme_order = 4 >> optimize_fft = yes >> ewald_rtol = 1e-5 >> tcoupl = Berendsen >> tc-grps = Protein Non-Protein >> tau_t = 0.1 0.1 >> ref_t = 300 300 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = Isotropic >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> gen_vel = no >> constraints = all-bonds >> constraint-algorithm = Lincs >> unconstrained-start = yes >> lincs-order = 4 >> lincs-iter = 1 >> lincs-warnangle = 30 >> >> I known this kind of error is not a priority since the total >> integration time is ridiculous big, but anyway I want to comment it to >> you. > > Yes, it's known. IIRC there was some discussion on the developers list about > changing the relevant data type so that it can store bigger numbers. It's > also a non-problem inasmuch as if you are ever able to run a simulation that > long, manually resetting the number of steps to zero at a suitable point > will be workable. > > Mark > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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/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/mailing_lists/users.php