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<br><br>> Date: Fri, 25 Sep 2009 08:23:37 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] BUG in GROMACS 4.0.5,        related to very log total integration time<br>> <br>> Daniel Adriano Silva M wrote:<br>> > Dear GROMACS users and developers.<br>> > <br>> > I don known if this issued had been previously addressed, but I found<br>> > that when I try to run a MD with time-step of 2fs and 2500000000 steps<br>> > (yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX<br>> > and icc 10 compiler):<br>> > <br>> > ####################<br>> > WARNING: This run will generate roughly 20576946697451257856 Mb of data<br>> > <br>> > starting mdrun 'F1-ATPASE'<br>> > -1794967296 steps, -3589934.8 ps.<br>> > <br>> > nodetime = 0! Infinite Giga flopses!<br>> > Parallel run - timing based on wallclock.<br>> > <br>> > #####################<br>> > <br>> > If i reduce the steps number by one order of magnitude then all goes<br>> > ok. My MDP when I obtined this error was:<br>> > <br>> > <br>> > ; VARIOUS PREPROCESSING OPTIONS<br>> > title = NPT simulacion<br>> > cpp = /lib/cpp<br>> > <br>> > ; RUN CONTROL PARAMETERS<br>> > integrator = md<br>> > dt = 0.002<br>> > nsteps = 2500000000<br>> > nstxout = 5000<br>> > nstvout = 5000<br>> > nstlog = 2500<br>> > nstenergy = 2500<br>> > nstxtcout = 2500<br>> > energygrps = Protein Non-Protein<br>> > nstlist = 10<br>> > rlist = 1.0<br>> > ns_type = grid<br>> > pbc = xyz<br>> > coulombtype = pme<br>> > rcoulomb = 1.0<br>> > vdw-type = Cut-off<br>> > rvdw = 1.0<br>> > fourierspacing = 0.12<br>> > pme_order = 4<br>> > optimize_fft = yes<br>> > ewald_rtol = 1e-5<br>> > tcoupl = Berendsen<br>> > tc-grps = Protein Non-Protein<br>> > tau_t = 0.1 0.1<br>> > ref_t = 300 300<br>> > Pcoupl = Parrinello-Rahman<br>> > Pcoupltype = Isotropic<br>> > tau_p = 1.0<br>> > ref_p = 1.0<br>> > compressibility = 4.5e-5<br>> > gen_vel = no<br>> > constraints = all-bonds<br>> > constraint-algorithm = Lincs<br>> > unconstrained-start = yes<br>> > lincs-order = 4<br>> > lincs-iter = 1<br>> > lincs-warnangle = 30<br>> > <br>> > I known this kind of error is not a priority since the total<br>> > integration time is ridiculous big, but anyway I want to comment it to<br>> > you.<br>> <br>> Yes, it's known. IIRC there was some discussion on the developers list <br>> about changing the relevant data type so that it can store bigger <br>> numbers. It's also a non-problem inasmuch as if you are ever able to run <br>> a simulation that long, manually resetting the number of steps to zero <br>> at a suitable point will be workable.<br><br>This issue has already been fixed for the 4.1 release.<br><br>Berk<br><br>                                            <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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