[gmx-users] version 3.3 - Range checking error
J.F.Hanna at warwick.ac.uk
Fri Nov 25 11:13:11 CET 2005
What I did was to use the files that were the output from a posres md 500ps run in v 3.2.1 (posres on protein, truc oct box spc water) and do grompp_d with v 3.3 and then mdrun_d with v3.3
The hardware and os details are:
node type: 1 x 1.6 GHz Itanium2 56-way SMP
interconnect: SGI NUMAlink4
OS: RedHat Enterprise Linux AS 3.0 / SGI ProPack
All code was compiled with:
and enable threads for fftw
I compiled fftw v 3 with the flags below, as there were no default flags for the intel compilers:
export CFLAGS="-ftz -O3 -tpp2 -no-gcc"
export FFLAGS="-ftz -O3 -tpp2"
The only messages i got during during gromacs v3.3 compilation that i was unsure about are:
checking dynamic linker characteristics... ifort: Command line warning: ignoring option '-p'; no argument required
ifort: Command line error: no files specified; for help type "ifort -help"
mknb_innerloop.c(362): warning #188: enumerated type mixed with another type
mknb_innerloop.c(363): warning #188: enumerated type mixed with another type
Hope this is what you were asking
Department of Chemistry
University of Warwick
J.F.Hanna at warwick.ac.uk
>>> spoel at xray.bmc.uu.se 11/25/05 10:02 AM >>>
Joanne Hanna wrote:
>I have recently tried to re run a simualtion with gromacs v3.3 in double precision that I have managed to run in v3.2.1 single prescision and v3.3 single precision. This simulations is failing with the following error:
Is this run with the same tpr file that works in single precision?
What kind of hardware do you run on?
> Step Time Lambda
> 104000 208.00000 0.00000
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 8.43377e+03 3.79108e+03 2.53005e+03 3.13091e+02 5.79138e+04
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 1.38869e+05 -1.05323e+06 -1.68330e+05 -1.00971e+06 1.91922e+05
> Total Energy Temperature Pressure (bar)
> -8.17790e+05 3.11754e+02 4.49698e+01
>Program mdrun_d, VERSION 3.3
>Source code file: nsgrid.c, line: 226
>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 5926. It should have been within [ 0 .. 5760 ]
>Please report this to the mailing list (gmx-users at gromacs.org)
>"Clickety Clickety Click" (System Manager From Hell)
>Could anyone please explain to me what I have done wrong? Should I have re-do the entire process with the double preision? i.e. from starting structure, solvate minimise, md with posres on protein to equilib water and then run my simualtion?
>Department of Chemistry
>University of Warwick
>J.F.Hanna at warwick.ac.uk
>gmx-users mailing list
>gmx-users at gromacs.org
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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