[gmx-users] version 3.3 - Range checking error

Joanne Hanna 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:
using lmpi
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


Joanne Hanna
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?
>Many thanks
>Joanne Hanna
>Department of Chemistry
>University of Warwick
>CV4 7AL
>J.F.Hanna at warwick.ac.uk
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
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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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