[gmx-developers] VFtab index too large

[David van der Spoel]

Chenyue Xing wrote:
> My neighborlist is set to be updated every 10 steps. It core dumped in 
> the 4th loop (outloop index n=4). From the printed-outs, in the first 
> 3 loops, the neighborlists seem to be stable.

if your atoms fly away there is something wrong :)
are you sure your forces are correct?
you should test the algorithm on a simple system and check for energy 
conservation.

>
> On 9/23/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     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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