Berk
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> Date: Mon, 13 Oct 2008 16:55:20 -0400
> From: [EMAIL PROTECTED]
> To: [email protected]
> 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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