[gmx-developers] VFtab index too large

David van der Spoel spoel at xray.bmc.uu.se
Sat Sep 23 09:30:14 CEST 2006

Chenyue Xing wrote:
> 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 helpful.
> I appreciate your responses!
> Chenyue Xing
How about your neighborlist? Is that updated as it should?

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