[gmx-users] Unexplained crashes with Gromacs-4.0
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 14 13:40:34 CEST 2008
Justin A. Lemkul wrote:
>
>
> Berk Hess wrote:
>> Hi,
>>
>> I don't really know what could be the problem here.
>>
>> 0..180 is (confusingly) not including the end, so 180 is out of range.
>>
>> The only thing I can think of (except for unknown bugs of coarse),
>> is that I corrected the coupling time of the Parrinello-Rahman barostat
>> when going from 4.0 RC4 to the official 4.0 release.
>> I guess all your old simulations were with older Gromacs releases.
>> So to get the same coupling as before, so would need to multiply tau_t
>> by 16.6.
>> I don't know if this would help.
>
> I did see this same error under RC2, but noticed that you fixed this bug
> shortly after I saw it, and that's what I assumed it was. But now I
> have seen it under the official 4.0 release.
>
>>
>> You did not get pressure coupling warnings before the crash?
>>
>
> There are no messages printed before this error pops up. What's really
> confusing is that if I simply try the same .tpr file again, it runs
> without a problem. I know that's not terribly scientific, but it seemed
> odd to me that my systems running for 40+ ns suddenly had a problem.
>
> Is there any diagnostic information I can provide? This problem seems
> like it would be elusive, since even I can't fully reproduce it.
That sounds like hardware problems, unless you use dynamic load
balancing which depends on timings and hence may make runs irreproducible.
>
> -Justin
>
>> Berk
>>
>>
>> ------------------------------------------------------------------------
>> > Date: Mon, 13 Oct 2008 16:55:20 -0400
>> > From: jalemkul at vt.edu
>> > To: gmx-users at gromacs.org
>> > Subject: [gmx-users] Unexplained crashes with Gromacs-4.0
>> >
>> >
>> > Hi,
>> >
>> > I've gotten the following error with two of my simulation systems.
>> Usually this
>> > weird "variable ci" error means the system is unstable, and I've
>> seen it before
>> > when I've done a poor job of equilibrating. But now I'm seeing it a
>> long time
>> > into my simulations (after 48 ns in one case, 60 ns in the other).
>> If I simply
>> > re-submit the job, it runs fine. The error shown is as follows:
>> >
>> > -------------------------------------------------------
>> > Program mdrun_4.0_mpi, VERSION 4.0
>> > Source code file: nsgrid.c, line: 357
>> >
>> > Range checking error:
>> > Explanation: During neighborsearching, we assign each particle to a
>> grid
>> > based on its coordinates. If your system contains collisions or
>> parameter
>> > errors that give particles very high velocities you might end up
>> with some
>> > coordinates being +-Infinity or NaN (not-a-number). Obviously, we
>> cannot
>> > put these on a grid, so this is usually where we detect those errors.
>> > Make sure your system is properly energy-minimized and that the
>> potential
>> > energy seems reasonable before trying again.
>> >
>> > Variable ci has value 180. It should have been within [ 0 .. 180 ]
>> >
>> > -------------------------------------------------------
>> >
>> > It seems to me that this "ci" variable is still within the range of
>> 0->180, if
>> > those values are inclusive.
>> >
>> > My .mdp file is as follows:
>> >
>> > title = NPT simulation for a membrane protein
>> > ; Run parameters
>> > integrator = md
>> > dt = 0.002
>> > nsteps = 5000000 ; 10000 ps (10 ns)
>> > tinit = 40000
>> > nstcomm = 1
>> > ; Output parameters
>> > nstxout = 50000 ; every 100 ps
>> > nstvout = 50000
>> > nstfout = 50000
>> > nstlog = 5000 ; every 10 ps
>> > nstenergy = 5000
>> > nstxtcout = 5000
>> > ; Bond parameters
>> > constraint_algorithm = lincs
>> > constraints = all-bonds
>> > continuation = yes
>> > ; Cut-off's and neighborsearching
>> > nstlist = 5
>> > ns_type = grid
>> > rlist = 1.2
>> > rcoulomb = 1.2
>> > rvdw = 1.2
>> > ; PME electrostatics parameters
>> > coulombtype = PME
>> > fourierspacing = 0.18
>> > ;fourier_nx = 0
>> > ;fourier_ny = 0
>> > ;fourier_nz = 0
>> > pme_order = 4
>> > ewald_rtol = 1e-5
>> > optimize_fft = yes
>> > ; Berendsen temperature coupling is on in three groups
>> > Tcoupl = Nose-Hoover
>> > tc_grps = Protein POPC SOL_NA+_CL-
>> > tau_t = 0.1 0.1 0.1
>> > ref_t = 310 310 310
>> > ; Pressure coupling is not on
>> > Pcoupl = Parrinello-Rahman
>> > pcoupltype = semiisotropic
>> > tau_p = 2.0
>> > compressibility = 4.5e-5 4.5e-5
>> > ref_p = 1.0 1.0
>> > ; Generate velocities is off
>> > gen_vel = no
>> > gen_temp = 310
>> > gen_seed = 7041776
>> > ; Periodic boundary conditions are on in all directions
>> > pbc = xyz
>> > ; Long-range dispersion correction
>> > DispCorr = EnerPres
>> >
>> > Any ideas what's going on?
>> >
>> > Thanks,
>> > Justin
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Graduate Research Assistant
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
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>
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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