[gmx-developers] VFtab index too large

Chenyue Xing cxing at ucdavis.edu
Sat Sep 23 08:59:11 CEST 2006

Hi David, Erik and other developers,

You might remember I posted several questions related to the C codes
(nb_kernelxyz) weeks ago.
I've been trying to make a z-dependent only LJ interaction.
Once I make rsq=dz*dz (instead of rsq=dx*dx+dy*dy+dz*dz), after a certain
number of loops and steps, the coordinates of one neighbor atom get quite
large (of the order of 10^5), making rsq even larger. As r is then used to
computer the index of VFtab, nnn, this leads to a nnn of the order of 10^9
and of course, the program cannot reach the memory address of
VFtab[1000000000]. So it goes to a segmentation fault.

I really don't understand why a small change in rsq (my system is a 128 DPPC
with water, total 4700 coarse-grained atoms, dx dy is usually around 1 nm
for each step as printed out) will result in a sudden bump of pos[] (or rvec
x[]) values. If you could shine some light on this issue, it will be very

I appreciate your responses!

Chenyue Xing
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