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

[David]

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.
________________________________________________________________________
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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