> Date: Fri, 25 Sep 2009 08:23:37 +1000
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] BUG in GROMACS 4.0.5, related to very log
> total integration time
>
> 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.
This issue has already been fixed for the 4.1 release.
Berk
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