[gmx-developers] Fatal error: ci = -2147483648 should be in 0 .. 7999 [FILE nsgrid.c, LINE 210]

David spoel at xray.bmc.uu.se
Sat Nov 15 11:44:28 CET 2003

On Sat, 2003-11-15 at 11:02, Martina Bertsch, PhD wrote:
> Dear GROMACS Developers,
> When running a CG-EM on a system composed of a protein embedded in a
> lipid bilayer, with no constraints and FLEX_SPC (see attached *em.mdp), I 
> get the following error message:
> Fatal error: ci = -2147483648 should be in 0 .. 7999 [FILE nsgrid.c, LINE 210]
> I figured that the ci is -(231) and the range of acceptable values is
> from 0 to 7999, for a total of 20*20*20 = 8000 cells in my grid, as shown 
> in the log file. I thought there could be calculations associated with the 
> grid that resulted in numbers greater than the maximum cardinality of the 
> machine word size (232), causing some kind of numerical overflow.
> A number of users have reported this problem in various contexts, and the only 
> solution that I have found is the fix for the minimize.c program, suggested by 
> Dr. Graham Smith (see the May 28, 2002 message to gmx-developers). Dr. Smith 
> actually   said
>  he used to get the same error message when running CG-EM.
> I implemented the fix and successfully recompiled.
> However, when I try running CG-EM with the same data set, I still get the same message:
> Fatal error: ci = -2147483648 should be in 0 .. 7999 [FILE nsgrid.c, LINE 210]
The error comes from coordinates being NaN (not a number). The physical
reason for this is that particles come too close to each other. Your
best bet is probably to check your starting structure once more: see if
you have lipids close to your protein. If you do steepest descents EM it
will print which atom has the largest force on it, so tht might be a
good starting point.

Furthermore you are using a cut-off with longer Vanderwaals than
electrostatic. Is that really what you intend to do?

David van der Spoel, PhD, Assist. 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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